Its a bit of a three-way-tie between xp, 2k3, and vxa for my top spot.
I like all three of them for their own purposes.
I have a soft spot for xp's wild (spaghetti) west scripting and layered mapping, but I do feel like vxa is the most competent and brimming with potential of the bunch, if only because it has a cleaner back-end than xp and has a robust set of tools in the database that seem to actually care about adding depth to the battle system. Despite this, vxa doesn't quite feel like home.
2k3 is my first love, but I recognize that despite its bells and whistles, it has its limits. Limits I adore, and limits I could stand to work around. The upgrades it got with the steam release definitely make it a contender though. Its fantastic when you don't wanna mess with scripts and wanna make an agile walking simulator, but the battle system leaves a bit to be desired in terms of variability. At least it has built-in side-view battles and actually works well for parallaxes..
2000, I managed to actually get a chance to work with in a recent floppy event, and after a while I just started missing 2k3's quality of life upgrades. its alright, but 2k3 is an upgrade in every sense of the word. Had to write a bat file to make the games run in windowed mode on newer machines due to its reliance on the old directdraw.
MZ sounds like an upgrade of MV, but still has a couple of the draw-backs that MV has, and requires the use of a complex effects system for animations. For those working in high-production values, it sounds like a good option, but for a hobbyist with a freaking day-job, it sounds like too much trouble for something that worked just fine in earlier iterations. (I also use animations for a lot of things that can't be easily put together in 3d!!).
MV is okayish, but I still like vxa better. I don't like 48x, I don't like javascript, I don't like the hard to reach documentation, and I don't like the hands-off feeling of the plugins. The project file sizes are also way too freaking huge for my tastes.
VX I can't give a fair assessment because I've avoided it like the plague (as someone who actually tries to avoid the plague :b ), but hearing about the obvious downgrades it has, it'd prolly find a place low on my list.