I've used nearly identical Deere tractors with the 9x3 Top Shaft Synchronized/SyncShuttle and the 12x12 PowerReverser. The TSS is a very traditional mechanical transmission that's been around for decades and if you've used older gear drive tractors, it will feel very natural to use. On the 5E tractors it can also be set up with a creeper, has a dry clutch, and still has a mechanical lever-operated PTO engagement. The PowerReverser uses a wet clutch, there is a reverse stalk on the steering column instead of a reverse gear in the gearshift, an electrohydraulic PTO engagement, and has a lot more electronics. The fourth gear in each range in the PowerReverser is probably the nicest feature of the PowerReverser transmission. There is a learning curve to smoothly operate the PowerReverser transmission and you'll probably wind up in or out of neutral when you don't want to at first. I do not particularly like that reverse in each gear is about 10% faster than forward where it "should" be the same speed such as in a CNH mechanical non-synchronized reverse lever (which I actually like a lot better than Deere's setup.) The 5E with the PowerReverser I've used does not have the modulator and it would be nice if it did have it to slow down the forward/reverse transition without clutching.
The 3 cyl 5Es can have two rear SCVs, two mid SCVs, and then one more on a diverter on the loader joystick. I recommend the two mid and two rear SCVs and would only get the third on a diverter if there was some very specific piece of equipment that required three SCVs and you didn't want to remove the loader. I'd loop a hose to one of the rear SCVs if I were running a grapple, for example.
I like the current hook-and-linch-pin Deere carrier better than the skid steer carrier. The skid steer carrier is more fussy to get seated correctly than the Deere carrier, I've used both.
The differences between the 5045E and the other 3 cyl 5Es is that the 5045E is only available with the TSS transmission, open station. The others can have either transmission and are available in a cab or open station. Standard rear tire sizes do vary with model with R1 tires (same for all models if using R3/R4s) but you can specify 16.9x28 R1 rears on the 5045E or 5055E instead of the smaller standard ones. Front tire sizes are also the same on all models for the same type of tire.