Is this the general consensus though- Thunder's offer improved/better flipping, based on geometry?
It depends on how you like your flip and pop to "work." Indys, esp. the standard 55mm Indys, are a lot taller than Thunders (inc., the new Team thunders, which are 1mm taller than standard Thunders). The result of that is a steeper angle on the the ollie/nollie, thus making them more powerful. There is some video with Prof. Schmitt and Spencer Nuzzi which explains the physics of it. So, as the theory goes, Indys will give you a higher pop than Thunders due to their height.
On the flip side (pun intended), with a lower truck, the tail hits sooner, thus allowing you start the flip on the board (e.g. kickflip, nollie flip, etc.) sooner. Is that better? It all depends on what you like.
One issue I have with Thunders is how
short the outer end of their baseplates are. Take a pair of Thunders and put a 53mm wheel on them, and push them against a wall; the WHEELS will hit the wall, and the end of the baseplate WILL NOT TOUCH. With Indys, the reverse is true (baseplate touches, but wheels do not). So, if you are doing a really locked-in nose/tail slide on Thunders, you need to wax the fuck out of the inside of the ledge
BECAUSE THE WHEELS ARE WHAT'S SLIDING. With Indys (or almost
any other truck), you can lock-in
against the baseplate, and don't have to worry about getting "wheel bite" during the slide. I can nose/tail slide much better on Indys than Thunders, because with Thunders my wheels always "catch," unless there is a stupid amount of wax on the ledge.
EDIT: I personally think the Stage 11 55mm Indys are too high, and the standard Thunders are too low. 53mm forged Indys, or Thunder Teams...you're in the butter zone.