They should have just ripped the continuity band aid right off and did a complete reboot.
I can't say I agree with much of your post, but this much I do. Half the first movie is inevitably going to be spent introducing the new cast, but having the other half explain some tentative connection to the prime universe was more than a little lame. Especially when they could've been telling their own story. That is the whole point of a reboot, so you can do things fresh and original. I just wish we'd have seen more of it in ID.