So which FFVII bosses will be in the third tier of Omega?

[Dualblade]

Kraken and Tiamat are automatically out though due to already being in the game (Kraken already is the final boss of not one but two dungeons - Hullbreaker Isle NM and Sastasha HM - and Tiamat is a HW story npc who is benign and definitely is in no position to be an enemy, being trapped in self-imposed penance in Azys Lla and all).

Given that its already been confirmed with Sigmascape that Omega is also pulling from other worlds for his tests (as Sigmascape has no real or fictional correlations to Hydaelyn, with the exception of Y'shtola having deja-vu when she saw the Kefka minion.) they could still use Kraken and Tiamat for it if they wished. Deltascape 3 in fact also proves this, as we have Halicarnassus there and in Hakkue Manor HM.

As for what possible fights we might get in Omegascape, I find it doubtfull we'll get another final boss from any FF game as O11, unless it turns out we actually aren't fighting Omega or if they surprise us with an O13. Diamond, Ruby, and Emerald weapon would all seem ideal as other machines that are "weaker" than Omega but still something that should be beyond our abilities according to Omega's maths. Various other bonus bosses could also be used, showing that we are going even further beyond the limits mortals have.

We have too many mega dragon fights already.

Twintania, Shinryu, Nidhogg, Bahamut. We're likely to get a few more in the near future (Seiryu, one of the 4 lords is a Blue Dragon; Koryu is 5th lord and is a Gold Dragon). Do we really need to fight another mega dragon?

Like dakka, there is never enuf dragon.