I think that the main difference between something like excadrill and gen 4 heatran is what actually counters/checks it. Heatran had a lot of checks/counters such that you could stop it in a variety of ways and didn't restrict team building. Excadrill and to a certain extent latios and thunderus don't. It's either carry X or lose a pokemon every time it comes in or in the case of excadrill it's carry gliscor or face the risk of getting swept entirely. The result is that every team ends up with X for latios, Y for thunderus, Z for excadrill and so on. We would have no troubles with kyogre either. Every team just need to carry a gastrodon like every team carries a gliscor. But that doesn't really make the metagame any good does it?
I think that was part of the intent of my original post, but I got distractd and lost my train of thought partway though it :P. thanks for clarifying it for me (even if I couldn't do it myself).
Heatran had many checks, things that should be Uber have few/none.