I choose XP, it has a very convenient scripting capability, as you said, Rm2k3dude, you only have to script it once, to make continuous effects, it also is very flexible, as, you can edit the scripts to make them what you want.
And, better yet, whilst importing, it no longer checks for the size of the image, thus, you can use one source [like, Game over screen] for something entirely unidentical to what it's made for.
The only down thing to XP is the double sized graphics, pokemon games would look very pixelated, due to this.
Yes, DarkMage, some of the built-in commands in Rm2k3 were removed in RMXP, a great example would be the Memorize Location Script. But, one expert, DubeAlex, has managed to create an identical script to that, so, I think, that Enterbrain removed commands which could be done in RGSS [The Scripting Capability in RMXP]
To sum it up, if you would like a more flexible engine, I advise you to use RMXP, otherwise, if you'd like, a simple, yet effective engine, use Rm2k3.
In my opinion, I would definately stick with RMXP
^ That was my evaluation :D