It's hard to say what would have made Hotline Miami a better game, but we can always speculate. How about the addition of a... gravity gun? Before you dismiss the idea, you might want to check out Half-Line Miami, an unrelated indie game nearing completion that's influenced by -- you guessed it -- Miami and Half-Life.
Does it work? Well, going by the trailer here it has potential. It's top-down and retro, like Miami, yet features the ever-silent Gordon Freeman. Rather than carrying around a horde of projectile weapons, Freeman has just the gravity gun, though there's enough junk sitting around that killing opponents isn't much of a problem.
Oh, and you can press "R" to restart. That seems worth mentioning.
The IndieDB page says the game's engine is custom-built, despite looking like a product of GameMaker. There's no release date, but barring any intervention from Valve or Dennaton Games, I can't see it taking too long.
Half-Line Miami [IndieDB]