Yes, it is a good decision to make a stable V3 compatible with V2 without new features. After that the PPC should be bored, so it needs input. The problem on 68k was that Tracker never got CPU hungry features because of the slow 68k. With PPC you have some more power to waste.

About your VST question: I`ve to say I don`t know because I`ve only heared about in theory. As far as I know there exists free and commercial plugins. Free (open source) can be ported/adapted without much work for you and other developers (yes, other should be able to wrote there own. You won`t have the time for it). An open interface would be necessary. First I would look on other systems to check out for later use. Then the decision is easier to select which plugin. I would love some filters, cut-off, resonance, distortion, compressor. Someone also like chip-sound generator or sample generator in general.