Well, my issues with it aren't really anything you can "fix", it's more of a foundational problem.. more like, "it's not the solution I would personally use, but I can understand why others would".
It might just be a difference in taste? Because when I look at the second preview image (with the additional modded planets), I can't help but think it looks "weird", yet I can't really place a finger on why. Maybe because the lines connecting the planets seem long and stretched? Or maybe because it seems very linear.. but that's kind of the point, isn't it? To smooth out progression by making it a little more obvious in which order you should tackle each planet. So then maybe it's because the solar system starts to look "gameified", if that makes any sense?
Oh, actually, I might be able to think of a few problems with it; interaction with "moons"? They are technically still "planets", but they generally only connect to their parent planets. Frozeta (moon of Secretas) seems a little odd directly connecting to another planet... Second potential issue, the space locations added by the Dyson Sphere mod (seen in the image above) might also pose a problem?
EDIT: Actually, I'll take those last two to your discussion thread instead; seems more appropriate