You're free to think however you like, but personally I don't feel that this is how one should look making games. Without getting into the whole schtick of indie vs non-indie, I'm just going to say that the game should come first. Not the engine. There's no sense in having a "main" engine that makes it harder to make the kind of game you're going for. Like, it IS possible to make an isometric turn-based tactics game with RPGMaker... but you would probably find it easier to do it with another engine (possibly a custom coded engine).
Similarly, you wouldn't want to be making a smartphone game with RMVXAce. You'd use MV for that, because that comes out the box with the tools needed for you to make the game run on Android/iOS (there are third-party/rumored proprietary unreleased tools for porting Ace games to mobile, but you'd have to put in extra effort to acquire and use them). Scripting-wise, both VXAce and MV are about equally as flexible. MV slightly more, because all the libraries are exposed and you won't need to worry about violating the terms of use like you would in Ace if you need/want to access any of the hidden RGSS DLL methods.
The main draw of MV's plugin system is really just making it more accessible for non-scripters to use, which isn't going to matter a whit to you since you can code. Plugins can still clash and, unlike VXAce's Ruby core library which is all contained in the RGSS DLL (minus some networking functions), JavaScript compatibility is dependent on the player/browser it runs in. Some functions may work in one browser and not in another (i.e. JavaScript's "includes()" function which will run in Firefox/Chrome but not in IE... or the stock Android browser). It shouldn't largely be a problem if you use MV but I imagine if it occurs it could end up being a headache.
Otherwise, it's just a matter of what you think will save you the most effort or will help more when making your game. If you can already code then any differences between Ace and MV's stock set of event commands won't be a big deal. You'll be looking more at resource formats, ease of porting your game, technical limitations (i.e. database entry limits, map size limits, ect.) and all that.
Once more, I advise you look at what your game needs first before you go looking for an engine.
Personally I'm playing with engines first before going to plan my whole game. I need to be familiar into some engines and plan around what i'm capable of. I'm not going to plan a game that I don't even know if I can implement its mechanics.
Anyway I just wanted to know the difference between them. I might be over-exaggerated the fact that it's gonna effect my entire life.
I'll keep your advice in mind~~