Only thing i could think off thats a bid odd on the pyra are the hitboxes of the topdeck guns. Its pretty hard to actually disable them even if your shooting a manticore you can somehow totally miss this guns.
Interesting you mentioned that, rumor has it that it will be fixed next patch. In higher level play that'll definitely knock pyra down a few pegs.
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The squid doesn't move the way it did in the past, but neither do any of the ships.
Do I miss being able to fly my pyra around like a fighter jet zipping all over the map, sure. Do I miss being able to make intricate turns and rapid altitude adjustments in my galleon, absolutely; and do I miss being able to put my squid in any area of 3d space whenever I feel like, of course.
I think we're all nostalgic for parts of the game we enjoyed months ago, double flak merc galleon was super fun to use when it was completely broken in 1.1, just like all sorts of other game mechanics, but at the end of the day, the game has changed and in regards to balance definitely for the better. The game is better balanced now than it ever has been as long as I've been playing goi. The squid has lost some agility but so have all the other ships and the squid has definitely not lost its edge. It's difficult to use, but definitely still competitive and can still 1v1 any ship in the game with the right loadout.