That's the funny thing about pilot episodes. They toss a bunch of ideas around, keep what works and ditch what doesn't. Guess Autbots flying was one of those things they felt didn't work. I wouldn't read into it any harder than that.
Sadly the Meleee weapons that Optimus & Megatron both used in the MTMTE episodes were never seen after those MTMTE episodes.
It seemed like various transformers had meelee weapons in the MTMTE episodes. I'm wondering how many transformers got to re-use their meleee weapons after the MTMTE episodes.
I noticed in one of the MTMTE episodes Ironhide on earth opens up his back vechicle door & another autobot uses the gun monted thing inside the van to shoot decepticons with.
Obviously we don't see that many of the first episode MTMTE cybertronian alt modes in other non-MTMTE episodes for the season one & two transformers. I think we only see the Cybertronian seekers on cybertron in other non-MTMTE Episodes.
FUNNIEST THING OF ALL: In one of the MTMTE episodes optimus prime was shown flying in the air & also shown making super flight jumps like superman. FUNNY PART,in that same episode that optimus flew in the air,optimus fell into a ocean/lake & needed Jazz's grapling hook to reel him in to safety. it's funny because optimus flew in the air in this episode,optimus should have been able to fly out of the water & into the air.