Well, honestly, VX Ace is still good. There are a lot of good reasons to stick with it, such as a more larger amount of resources, both commercial and free, Ruby is easy enough to learn to script with than Javascript and honestly with MV, you need a more powerful computer to run the games with due to them being made in HTML5, which is not older PC friendly.
The advantages of MV are that, as Andar stated, it has a much better window size without resorting to messy glitches and it's more portable in terms of platform distribution. The downsides is that Javascript has a slightly different learning curve and MV resources are still technically scarce by comparison because Ace can use XP, VX and its own resources without much modification.
They can still be used in MV at their native size, but you need plugins to change the way things are displayed at runtime. I still highly recommend VX Ace alongside MV since they are both very good engines. Choice is yours, really.