Honestly I think that's way too broad. A lot of things can be considered similar to each other when you go for the broadest levels of description.
As it stands though, I don't agree when you look at the subtelties.
1. The suit:
While Gordon Freeman and Masterchief both have powered suits, they are different. Masterchief's suit for instance has regenerating shields whereas with Gordon you still require healthpacks. Conversly Gordon Freeman can actually swim in his suit whereas Masterchief sinks like a stone.
In all seriousness though, the idea of a high powered super suit goes all the way back to the early Metroid games and Megaman. I doubt there's any real connection here that doesn't also apply to almost every sci fi action game ever.
2. The alien invasion
Alien invasions are also often seen in games, Resistance, Gears of War, Crysis etc. It's not like Halo and Half Life stand alone in this respect. That said even then the way the aliens invade is too different.
Going by what I understand of Half Life, the aliens came from a planet that was given access to Earth via a wormhole in Gordon Freeman's lab at Black Mesa.
The Covenant meanwhile are a huge galactic empire in the distant future who, rather than starting at Earth, ended at Earth having destroying all the planets and colonies belonging to the human race first.
And the universe thanked them.
But seriously, there is a difference. Plus I'm not sure about the Combine but I know that the Covenant were religious zealots and were essentially a riff on the idea of zealotry in religion, taking inspiration from both eastern and western religions in the way their culture was designed.
Meanwhile I hear the Combine use actual brainwashing.
Plus I don't recall Half Life ever making us take the role of a Vautigaunt midway through the story to see thing's from the Combine perspective. But they did that in Halo 2 with the Arbiter.
3. Friendly NPC's.
There are NPC's in almost every game ever made and although the marines, grunts and Elites that you find yourself temporarily allied with over the course of the games have some personality... they aren't as fleshed out as the ones in Half Life. They are simply disposable extras.
Unless we are talking about the plot important ones, The Arbiter, Cortana, Johnson, Miranda Keyes, Captain Keyes, Rtas Vadum, 343 Guilty Spark, Lord Hood etc. But then those are the main characters in the story, not just random NPC's.
4. Headcrabs=Flood?
Again, alien parasites aren't a new thing in games. I mean Dead Space has probably the best version of 'the Space Zombie' in gaming history and that's the Necromorph. But as for the headcrabs and the flood, there are certainly similarities in the way they are designed and how they interact and how they infect people. But also in Halo the Flood form hives by creating a fungal growth on the walls of places they infect that becomes alive. We also see flood 'pure forms' running around which are just the flood fungal growth made into sentient fighting creatures. They also seem to have a central hive intelligence called 'the Gravemind'.
Admittedly I don't know much about Headcrabs but aren't they essentially just crabs that turn people into zombies?
I admit there are similarities but there are still differences.
5. Both games have linear encounters.
You said this one was obviously a joke so I'll disagree here.
Anyway to round it up, I don't see much similarity between Halo and Half Life. Mainly due to the fact that I loved Halo very much and it is probably still my favorite game series to date, whereas I could never get into Half Life.
Person preferences I guess. Either way in my brief time playing Half Life 2, try as I might, I couldn't see the excitement factor. I just ended up playing the hell out of Portal instead.
In any case, I just don't see enough similarities to say that Halo was inspired by Half Life. Because those factors can apply to all games, even games that predate Half Life and that come after Halo.
But flood also takes something from Tyranids and Zerg AND obviously Half-Life headcrab design 
