JEMay

I'd go with the left side, but they look like they have been processed differently.  If you chose a film setting for the jpeg, why didn't you process the RAW to look as close to that setting as you could?  Have you ever seen those contests that one of the preset companies puts on?  I think it's Mastin, where they post an image and you are supposed to guess which one is film, and which one is processed?
 
And this still doesn't address my statement.  I never said the jpegs were bad.  I said you shoot RAW so you don't get the compression of the jpeg, and you have more latitude with processing.  However I also shoot RAW+Jpeg.

I shoot both out of sake of security, if I mess up my exposition on the Jpeg, I can always use the RAF file.
 
But really, every single time I take a look at the Jpeg files out of the camera, it really makes me wonder why I am spending time to lightly retouch my pictures to begin with.
 
Let's play a game, the Fuji regulars will find it quickly but can you tell which side is processed RAF and which is the Jpeg directly from the camera ?
 

The Jpeg's are good, but it's my understanding that RAW shooters don't shoot RAW because the Jpeg's are bad.  They shoot RAW because they don't want the compression, and the settings locked into the file like the Jpeg's are.
 
Or am I just missing something?

I shoot JPEG + RAW but almost always edit the jpeg a bit and keep the raw just in case.  The good thing about shooting jpeg+raw is that if you shoot black and white, you will always have the raw file if you want a color version of the shot.  If you go with just jpeg when shooting black and white, that's all you get.

Some examples of straight out of camera JPEGs from me
DSCF2037 by Will Solis, on Flickr
 
DSCF4648 by Will Solis, on Flickr
 
90mm F2 Fujifilm! Straight out of camera by Will Solis, on Flickr

I've been shooting raw (like that frizzy hair guy on YouTube) for a long time now.  Nikon, Olympus, Sony, Panasonic, an older Fuji (X-Pro1 and X100S) and maybe another brand I forgot ;-)...but I've always been shooting raw since I discovered editing in Lightroom (version 1).  I've always been more happy with raw since it was much easier to adjust white balance, push/pull shadows/highlights and various other reasons.  Mostly for flexibility and highest image quality.  
 
Well, after about a year and a half with the X-T1, I think I'm finally going to shoot JPG only (except for rare occasions).  Why?  I just can't replicate (in Lightroom) the great color and tones I get straight from the camera.  I've tried for awhile now to tweak the Adobe provided camera profiles to my liking, but they always seem to have too much contrast and the color just isn't quite the same.  
 
Adjusting white balance in Lightroom?  The X-T1 has the most accurate auto white balance I've seen from a camera.  I previously gave that nod to the Olympus E-M1.  So, adjusting white balance for my Fuji files isn't as important anymore.  
 
Recovering highlights or lifting shadows in Lightroom?  That's not as important anymore either because I've editing the in-camera settings to my liking so that I don't have really harsh shadows or highlights.  I can tweak a little here and there as I see fit for the JPG files in Lightroom.  
 
I went outside around my yard and garden and snapped some examples over the last day or two.  I'm very pleased with the images straight from the camera and with a few mild edits in Lightroom.  These are all from the 56mm and 18-135mm.  Some people badmouth the 18-135 being just an average lens at best, but I think it's excellent.
 

 

 

 

 

 

 

 

 

 

 
 

Haha! This was definitely a "can't see shit captain" lighting situation. In fact, I had to use a video light to identify which lens I was pulling out of my camera bag it was so dark!

You forgot to mention the most important part: Fuji will let you frame the shot and see what's going on way below light levels at which the naked eye goes into mysterious realm of "Can't See Shit Captain".

One important distinction that may be worth clarifying is that the ability to "change the ISO with command dial" on X-T10 is probably not what you think. It's not that you can set the dial to directly change the ISO, it's that the command dial on the X-T10 is ALSO a function button (when depressed) and you can set THAT to be ISO, then use the dial itself to change the value and depress it again to confirm. 
 
On the X-T1 the equivalent would be to assign ISO to the front function button, since it exists to replace the "missing" function button on the dial which can't be depressed on the X-T1. You'd have to use the function button AND the dial in that case, just like if you assigned ISO to the back function button on the X-T10. 
 
As pointed out it's mostly irrelevant because Fuji chose to not allow ISO as a function button on the X-T1, presumably because the complexities of overriding the mechanical dial were too complicated to execute or deemed too complicated for users to have to deal with. 
 
Personally I prefer the X-T10 system because like you I found the X-T10 ISO dial simultaneously too tedious to use and too dumb to reflect what I really want to do, which is switch between AUTO-ISO configurations rather than absolute ISOs.
 
90% of the time I can get my ISO right just by changing between the auto-ISO options, but the X-T1 makes it really hard to do because there's no function button for it and the Q menu doesn't show what's IN each auto-iso config, only it's number. On the X-T10 the ISO function button menu shows you the "contents" of each auto-ISO config as you scroll through them, which to me is the ideal functioning. 
 
I wish the X-T1 ISO dial had positions indicating the auto-ISO slots, THAT would be useful. Ideally you could switch between them and as you do a graphic would flash on screen indicating the parameters (max-ISO, min-shutter) for that auto-iso slot. This would give the best of both worlds and personally it would redeem the ISO dial in my eyes. 
 
Of note: The way it REALLY should work on both cameras is that they let us configure the front command dial to change settings directly, so we could just spin it to change the ISO rather than having to push->spin->push to change the value. That would match how Olympus and Sony make the dials work and would speed up usage significantly. Currently both the front and back dial have confusing and rarely-needed effects on how the auto-exposure chooses values, which I'd rather disable entirely, let alone be able to set the dials things I actually want (ISO, focus modes, shutter modes).
 
On the thread's subject line: "Firmware not the same"? 
 
Just to get back to the inherent question the answer is that the firmware has MANY differences between the two cameras that I never realized until I started posting my experiences with the X-T10 here and got confused responses from X-T1 owners. A lot of little things were improved in the X-T10 firmware but went unchanged in the updated X-T1. None are really important that I've found so far, but some are really valuable updates in my eyes. Either way, anyone who assumed (like me) that the firmware was basically the same thing running on two bodies turned out to be wrong, they are different operating systems that happen to have most of the same features. 
 
The best example I can think of now is the Face Detection button, which on the X-T10 just enables/disables FD directly, but on the X-T1 brings up a stupid menu with only two options, tripling the number of button pushes needed to use it and forcing you to use the D-pad rather than just the one function button. A super valuable update if you use FD and I find it hard to understand why it wasn't backported to the X-T1. 
 
The ISO menu is the other example I can think of but as already stated, it has a better reason for not being there: The physical dial. 
 
Overall my most charitable guess is that the updates they didn't backport to the X-T1 were left out because they didn't want to "change" things they didn't have to. Maybe Fuji believes people who have had the camera for year(s) and are used to them don't want to have to learn new behaviours (like the FD button) even if they are better. I humbly disagree if that's the case, but there's a logic to it.

It doesn’t work, no AF-improvement, it doesn’t focus between each shot in CL or CH, no faster AF in low light! This is some of the negative feedback we could read in the comments on FR and at the Fuji-X-Forum here.

So what… is Firmware 4 just crap? Well, sometimes (often?) it’s just a matter to find the right settings. Patrick has made up an extended list of tipps:

Enable Mechanical Shutter (MS) only. The camera won’t focus between each shot in CL or CH tracking, if ES only (electronic shutter) or MS+ES is enabled. Shooting fast-moving subjects with the ES doesn’t really make sense (rolling shutter effect).

Turn Off Face Detection! If you have Face Detection put to ON, the camera will focus only with CDAF. The faster Phase Detection AF (PDAF) works only if Face Detection is disabled.

High Performance Mode ON: many don’t even know that this features exists, like Calipedro here. It’s definitely worth to sacrifice a bit of battery life. Fuji should put this feature ON as standard.

Keep you subject in the center: Phase detection pixels are located in the center of the sensor. Keep your subject in the center and PDAF will give you a faster AF.

Use all Phase Detection Pixels with Zone AF 5×3: To take advantage of all the phase detection pixels, set you Zone AF box to 5×3 and place it in the center of the frame. Within this 5×3 box tracking will be very smooth… at least that’s my experience with my crazy dog.

Increase the size of the AF-box: If you use Single Point AF, increase the size of the AF-box as much as possible.

PRE-AF: The camera will continuously adjust focus, even if the shutter is not pressed (of half pressed). This can help to get the first shot in focus quicker. Downside: more battery drain.

LENS FIRMWARE: make sure that your Fujinon lens is updated to the latest firmware version.
 
Different Lens, Different results: According to the lens you use, the AF-improvement will be more or less (or not) visible. For example, I was very happy with the improvement of my 55-200, but I can’t really say if the 18-55 or 14 has become faster.

The learning curve: Practice and get used to the new features. See what works best in which situation

Let Rico study for you. Rumors has it, that Rico will update his X-T1 book and tell us how to make the best out of our new Fuji X-T1 FW 4. Once it’s out, all we have to do is to read his updated book.

So, do you have more tips? Then share them below!

Unfortunately it's not the camera, it's a light source. It's flickering pretty badly.