Trek. Let’s compare the people first.
The marvel guys just have one genius. Cap isn’t dumb just not at the same level as any of the trek
Fury? Eh. Picard wins hands down. Picard is a smart guy and understands his engineers and scientists. Dude didn’t serve across star fleet like he did for being dumb. Fury is a good leader, and can be more coy. I’ll say military prowess is also great, but Picard military knowledge trumps it by 200years.
Trek team has Data, a fucking Android who computes faster than any human alive and probably just as strong as cap. He covers the entire Marvel team himself.
La forge is probably on par with Stark if not more so. But he’s got data who he can bounce engineering ideas off of to a depth Stark can’t.
TNG crew have time travelled way more than Marvel as well, have also encountered other travelers.
Sure I’ll give marvel they may have some alien encounters and a very limited time travel understanding, and some ok tech. But honestly, You think Thanos was bad? Dude needed jewelry to copy what Q could do on a whim.
Now we can’t really compare cause in Trek, the Marvel enemies and advancements never existed. So we’ll look at in parallel universes joined for this war.
Marvel side: military leader, scientist, body builder. Trek side: military leader and explorer and scientist, scientist, android scientist
That said let’s look at how Picard and Fury would stack as leaders. Picard has 27 first contacts, including Borg, Q, Ferengi, is a regular political attachment for judicial and peacekeeping missions, and has gone undercover for for infiltration into hostile territory. Also speaks French and English. Looks at galactic level peace. Fury was a spy who later became director of a secret organization. His Job was to keep alien artifacts and other stuff hidden from the world and to build a team that protects the world. Fair. He did help the Skrulls. But all I’m all not a great negotiator or transparent in his actions. Picard wins for leader.
Encounters: I’ll say the marvel encounters are rough. Cree and the worlds we see in GOG are bad, but these three didn’t experience much outside the battles on earth and that one thanos battle with a moon crashing. Trek wins experiences on encounters.
Tech: trek wins. Data is about 1060 years ahead of whatever tech is available on the planet at 1213, and has encyclopedic history in his head, while also being incognito. He’d be able to detail every encounter and the generals to make sure they follow the prime directive while ensuring the truce is signed at Chinon.
Battlefield fights: Stark can’t suit up in 1213 with nano bots without utterly fucking a timeline, unless it can look like regalia. Fury can’t use his alien eye. Cap could medevil armor up and go out and just look and do something amazing without drawing that much attention. Picard and co wouldn’t be on the field. They end up as officers using data’s knowledge and military tactics to ensure wins. Marvel and co may do the same however.