You are quite wrong about Rebuild/Oge in my experience. When you hit Rebuild, you are already getting to 5 coin hands and the game is about buying/gaining duchies to Rebuild into Provinces. It takes two plays of Rebuild to bump Oge up to duchy, which is a bit faster than than the three required to turn the Estates into Duchies, better the +1 card off the first hit make it easier to buy something useful (like a duchy).
Some more general shelter points:
Limiting the number of estates hurts all the VP based attacks - B-crat is even weaker in the opening. It takes a LOT longer for Rabble to really hurt (barring curses); Fortune Teller is actually weaker against Shelters - in the early game it has good odds of reshuffling and getting your new better cards into circulation faster. Jester also loses some oomf as you have 2 immune cards.
Tribute and Xroads also play slightly differently as the initial card types have changed a bit. Xroads in particular is rarely useful for draw even in the mid game without estates; however with Necro, a Xroads or two can let you play a 4 or 5 terminal mini-engine deck. Transmute, already weak, gets even crappier without estates to target.
All of the scaling Tfbs get weaker (Bishop being, perhaps the lone exception). Even something like Trader takes a beating as an opener with Shelters out.
A few other big things about Necropolis:
1. You can much more confidently open double terminal. Odds are already against non-drawing terminals colliding in the first shuffle, but with Necro out the possibility is even more remote. Necro also makes it much strong to open trashing/terminal as you will be able to play both even after your deck gets thinned down - even if you buy some silvers for a bit.
2. It makes village denial harder. Take the obvious example of a Goons engine. The number of Goons you can play is often determined by how many villages you can buy. Winning the Goons split 6:4 is nearly useless if you lose the village split 4:6. With Necropolis you can play 5 Goons to your opponent's 4 and that is a win in the long term. Necropolis means that it is harder to deny +action to some engine that relies on lots of terminal action plays for draw, payload, or both.
3. Necro boosts limited draw like Jack, Watchtower, and Lib out of the gate. In like manner, Necro is quite nice for Peddler, Horn of Plenty, and Conspirator.
4. Necro does mean you can reliably dump a second terminal into non-terminal draw engines. This can be quite spectacular (e.g. militia/masq), but more commonly let's you do something like have a +buy and an attack or an attack and a light trasher both running.