I agree about all those potential problems regarding a time skip, but overall I'm not that worried about it. Narratively it's often used as an easy solution, but it's reassuring that she's planned it from early on in the development, and probably has a clear plan for what she wants to achieve with it.
I remember from playing GGGB that I thought it would've been fun to play further on some of the routes after seeing them in the epilogue. Of course, with a porn star or gang leader Ashley it didn't feel like there were anything more to do, but some of the more wholesome routes could have gone on for longer, in my opinion.
In general, I think one weakness for a lot of these kind of games is that they're limited to a very short period of time. One of the few other playable games on this site, Being a DIK, has been in development for a few years already, and has a lot of content, but it still only plays out in a few week. My guess is Eva wants to delve deeper into the relationships than GGGB and similar games do, and I think a time skip is a fair way to achieve that.
It does however place some massive demands on the storytelling. If all the strings aren't properly tied together and if there's events during the time skip that aren't adequately foreshadowed or implemented in the game, there's a big chance people will be disappointed because the characters are doing things they didn't want them to do.
To sum up: A bad time skip could really fuck things up, a good time skip (and that's way more difficult to write than a bad one) could really raise the game another level.
(Edit: Sorry for the initial half finished comment, I accidentaly hit "post" and was then disturbed before I could write the last couple of paragraphs.)