First and foremost, I just want it moved to campus sites. Neutral sites work well in the east, not so much in the west. Because it doesn't make sense to go campus sites with four team pods, as you're left with the same issue as a neutral site if the home team loses, it would be eight head-to-head match-ups in the first round. To me, if you're bringing a team from Ithaca to East Lansing, you might as well play 2 out of 3 than do all the travel for a single game. And as I said before, it's a series-based sport. The next round is the same situation, so it's another 2 out of 3 series at a campus site for the second round.
You have a point about arbitrarily going to single elimination at a certain point in the tournament, but that's just how college hockey has been, going to single elimination for the semifinals and finals. Plus, if you want to keep the Frozen Four, that doesn't really work in a series format. I guess you could just make the championship series the new Frozen Four at an NHL arena, but I don't see anyone going for that, whereas there does seem to be sentiment to go back to campus sites among some of the coaching community.
As for why no one complains when the #1 hosts, why would they? They earned it through their play throughout the season. An argument could be made that the neutral site should be truly neutral and their reward for playing well is getting to play a 4 seed, but since it's nearly impossible to have a true neutral environment, then it makes sense that any advantage should go to the better team.