XP has a similar problem. My theory is that the issue stems from the fact that RPG Maker is just a translation of the original Japanese version, which had users input the text in characters rather than our alphabet, and the textboxes were sized accordingly.
Anyway, as far as a solution, the simplest would be to just avoid using long phrases in text boxes, and use lots of line spacing. This is actually a good practice anyway, as dialogs are easier to read when they're given in small chunks; take a look at any popular RPG series such as Final Fantasy - they never hit you with a wall of text like that.
Of course, if you've already completed a significant portion of your game and don't want to have to re-space the text boxes, you could always use a script that allows you to change the font to a smaller size. This would also alleviate the issue. In XP, the UMS is of course the script I'd recommend; I'm not sure if there's a VX equivalent.