Personally I subscribe to the whole "core of the ship" belief in regards to why the bit TerminatoReaper at the end appeared human. It is just a "Larva" and metal doesn't grow, so that presumes that something (a "cocoon" maybe?) will be built around it in time.
The decision not to blow up the relay is possibly a plot hole, but probably not. Consider the size of the full relays and they are comparable in size to, perhaps, and arm of the Citadel. Cerberus simply doesn't have the firepower to take down something like that (remember, they have all of one known frigate and most of their resources have been pumped into you and it, so they can't have a large fleet of their own). The thing presumably has defensive barriers as well that would protect it from small attacks. Perhaps a combined fleet from the Council races could easily destroy a relay, however, the Council 1) doesn't believe in Reapers, so would not commit resources to randomly destroying a relay and 2) won't send a full fleet into the Terminus Systems, where the Omega 4 relay is located.
Besides, the Illusive Man wanted to evaluate and obtain the tech of the Collectors as much or more than he wanted to stop them initially, so it makes sense that the only option that HE sees is to go through.
What we accomplished in ME2 was, without question, the saving of millions of human lives being harvested by the collectors. That is a worthy goal in itself. We also stopped the creation of a new Reaper within the galaxy that could have (though there is no confirmation) had some effect on the speed with which the full Reaper fleet could return, one way or another. We just don't know. Certainly there can't really be much question that we "accomplished" something worthwhile and that the current arc of the overall story was well wrapped up.
As someone else posted, the real plot hole is "WTF is up with Banes and why did that storyline dead end in ME1?"
The decision not to blow up the relay is possibly a plot hole, but probably not. Consider the size of the full relays and they are comparable in size to, perhaps, and arm of the Citadel. Cerberus simply doesn't have the firepower to take down something like that (remember, they have all of one known frigate and most of their resources have been pumped into you and it, so they can't have a large fleet of their own). The thing presumably has defensive barriers as well that would protect it from small attacks. Perhaps a combined fleet from the Council races could easily destroy a relay, however, the Council 1) doesn't believe in Reapers, so would not commit resources to randomly destroying a relay and 2) won't send a full fleet into the Terminus Systems, where the Omega 4 relay is located.
Besides, the Illusive Man wanted to evaluate and obtain the tech of the Collectors as much or more than he wanted to stop them initially, so it makes sense that the only option that HE sees is to go through.
What we accomplished in ME2 was, without question, the saving of millions of human lives being harvested by the collectors. That is a worthy goal in itself. We also stopped the creation of a new Reaper within the galaxy that could have (though there is no confirmation) had some effect on the speed with which the full Reaper fleet could return, one way or another. We just don't know. Certainly there can't really be much question that we "accomplished" something worthwhile and that the current arc of the overall story was well wrapped up.
As someone else posted, the real plot hole is "WTF is up with Banes and why did that storyline dead end in ME1?"