It's fairly common to hold on to windows after their initial creation (I'm not sure any NI windows are truly disposed in code). I didn't know anybody would open 15 windows at the same time (unless you're talking about 15 open/close sessions, but that shouldn't be killing NI for you). I suppose it can be looked at, but there aren't any places I'm aware of where memory is handled manually (is it even possible with Java?).
Resource filename search sounds OK, but it would require changes to the interface, and I can't think of a svelte way to do it. Note you can search for "No such index" and similar to pick up no-string files. Attribute reference searcher also allows you to search for the current selected field across all resources of the same type. (So, if you already know the filename, I'm not sure why you're needing to search for it.) I believe you can also use the Open File command to select the filename from a list of available resources.
I believe we currently load a PLT file by itself without any creature association (meaning, there are no colors to pick from). There could be color pickers for every single location, I suppose, but I don't know how useful that would be. I agree that putting the ToB animation palette BMPs there is totally pointless.
As with window management, I don't think we can manually adjust memory at runtime, so no preference to set the memory level. Yay, Java! You can start the VM with -Xms (start; try 64M) and -Xmx (max; try 128M) to make Java use more memory.
We don't do anything special with the fonts (you get a list of fonts that are accessible to Java by default). I don't know how we can call out to fonts across all three platforms, but it doesn't sound like something that would be impossible.
Yeah, the game history menu is pretty bonky.
Probably no for the potion checker (it's easy enough to do this in WeiDU). NI supports all the different Infinity games, and they all use different usability rules, so it would be a bunch more code than just creating a checker with WeiDU for exactly what you want.