VX Ace or MV, hands down. 2k3 is great for that retro feeling, but the engine is not customizable by scripts or plugins, so you have to get handy with eventing if you want to go beyond the limits of the engine. 2k3 is also a lot more stringent on what resources you can use and how--every last image you put in the game has to be in indexed 8-bit color. XP has more flexibility than 2k3 with scripting, and with any other engine with mapping, but mapping in XP is considerably different than mapping in VX Ace or MV.
Between VX Ace and MV really depends on a few things, in my opinion.
- Battle system. If you're not going to spring for plugins or scripts for battle systems, then you have to choose between front view-only turn-by-turn (VX Ace) and front or sideview turn-by-turn (MV). This depends on your wants and needs.
- Distribution options. For Windows, unlike VX Ace, MV does not either automatically package the RTP (default resources) with the completed project nor leave them out (so your players also have to install them separately for the game to work). MV also has a lot more options with regards to distribution and games made using it can be played online (in a web browser), on mobile (if you know how to do that), and on Windows, Mac, and Linux. "Technically" you can use VX Ace on the latter two, but it requires a lot of workarounds and results can be kind of buggy. MV wins this category.
- Your operating system of choice. Do you use Windows? If you use 7, 8/8.1, or 10, you can pick either engine. If you use Vista, then your only option (without changing OS) is VX Ace. Do you use something other than Windows (like a Linux distro or a Mac)? Then go with MV, because it's built to work in those operating systems as well. MV also wins in this regard.
- Resource needs. Will you be making all of your own art? Are you content with just using the base engine, nothing extra? In those cases, it doesn't really matter unless you want the larger variety of settings MV provides for. VX Ace has more premade resources (graphics, sounds, scripts) by a long shot. However, using scripts is not streamlined into the program, so if you want to modify a parameter you have to edit the script itself in the engine. MV has a good selection of plugins already, and the engine being built more openly means plugins can be a lot more powerful than VX Ace's scripts. Overall, due to the larger range of resources (and, if you have licenses for VX and/or XP, you can use resources for those without resizing them), VX Ace takes this one for sure.
- Building needs. Basically, how you make your game with regards to graphics. MV has a higher resolution and thus seemingly higher-"definition" graphics. MV also has a better character generator than VX Ace and comes with a larger variety of tilesets, enemies, battlebacks, and other default graphics (you can make a modern or futuristic game using default MV tiles). Mapping is also easier in MV because you have a third layer to work with (and because of plugins like Yanfly's Grid-Free Doodads, which gives you a huge amount more flexibility in mapping). But, I mean, neither can compare to XP in this category using the in-engine map builder. If you decide to use parallax mapping, where you create the map outside the engine, MV and VX Ace are about equal. MV currently has a memory leak issue that can be worsened by the use of parallax maps, but there are already good fixes for it and it will be officially fixed soon.
- "Unique" battle system. Really depends what you mean by this. Unique generally does not mean easily-implemented. For a bullet hell battle system like in Undertale, consider all of the things you have to manage while building it: where the character's icon is, how it moves, where it can move, how quickly it can move, how each enemy's attacks move and work, what enemy attacks can and cannot do, displaying the character's HP, displaying the enemy's HP, implementing the accuracy/dodge mechanic (which I don't even know how to set up), and coordinating the battle transitions as well as images/text displayed within the battle. Side- and front view battling is built into MV, while only front view is supported in VX Ace without the use of outside scripts.
Really, I'd recommend trying out the demos for VX Ace and MV and seeing which you like better for your workflow. Both of them have great customization options and a wealth of resources. If you have Windows, it's really down to how you go about making a game and seeing which one is more or less useful to complement that. If you don't have Windows, I'd definitely recommend MV over trying to bend over backwards and fiddle with making VX Ace work outside of Windows (which is very very difficult if you don't know what you're doing).
