I own all the RPG Makers [except the console ones and the illusive RM95] And throughout them all, I have my favorite 'feature' list;
RM2k3: The SV battler animation system, there is so much you can do with this version of RPG makers side view battle system. And Every Weapon in your game could have a unique Sprite/Animation if you were so inclined to do an art.
RMXP: 3 Layer Tile Mapping, using this and the event layer together in harmony, with the exception of just flat out parralax mapping, is the most detailed you can get with the basic mapping features found throughout the RPG Maker series. As well as the Fog option.
RMVX/VXA: I honestly haven't used this one much. When it came out I tried it, but it simplified the tile mapping and I wasnt fond of the suddenly chibieverything characters. I like the Icons. >.>;
RMMV: I would have tucked this under RMXP as it was introduced there but; Scripting, Being able to do so much more than just the base engine is amazing and its what a game design engine needs. Aside from that, Portability. I don't use them, but Mac OSX support is great to see, Exporting to HTML5 and from there being able to release to any platform [that can handle HTML5] is fantastic as the mobile world is ever growing.
On topic; I still play with the older RPG Makers, I like them, they've provided me with a lot of entertainment and joy over the past 15 years. But for now, I am primarily sticking with MV. It's still got the new software scent, and With the way they have it, I think seeing expansion on what the editor can do naturally will expand. [Like weapon animations... Why only 6 user defined slots? 5 if you count the fact that a book is in slot 1.]
I think I was going somewhere with this... but it's New Years eve... and... rum drinks. :D