If you take both amps and run them through the same cab, the differences will be minimal. Mesas don't rely on power tube distortion for their signature sounds. A clean 6L6 is going to sound very much like a clean EL84 when they both have the exact same preamp in front of them.
That said, the biggest difference is going to be headroom, as in how loud you can play without the power tubes breaking up. The larger 6L6 tubes have more headroom. The new multi-watt feature of the Plus models is pretty awesome, though. I have a 5:50+, but I always run the channels in the middle 25 watt position. For some reason, I just prefer the sweetness that position provides. I have also been enjoying the Burn mode of the 2nd channel in 5 watts. It gets this nasty fuzz tone that I'm having a lot of fun with.
Now, my first Mesa was the original Express 5:25. Mine was the little 10" combo. I really regret selling that thing. It had a cool, unique sound when running through the little speaker, but when plugged into a larger cab, it really filled the sound out. I actually compared it against my dad's Mark IV one time, running them both through the same cab for a fair comparison, and I totally preferred my "cheap" 5:25.
I want to reiterate that the size of the cabinet makes a HUGE impact on the tone. If you only compare the 5:25+ combo to the 5:50+ combo, the 5:50+ will sound fuller with a better bass end. The difference you are noticing there is the larger cabinet. You could easily put the amps side-by-side, run them into the opposite cabinets, and hear the difference for yourself. (I think the 5:25 also has a Vintage 30, as opposed to the C90 in the 5:50. That will make a difference, too.)