If anything, strong female characters are impeded not because of the desire to avoid Mary Sues, but because of the tendency to make them “badass” with nothing behind it.
Ripley was tough and smart. But she was also human and lucky - and she knew it. SHe would not have gone out of her way to fight an alien. She was a realistic badass and worked in context of those films.
What annoys me are thing like the Tomb Raider movies, where we get the bland, obnoxious Lara Croft. Her personality is little more than one-liners, she’s simply a random superhuman badass who fights people (For ARCHEOLOGY!). Basically, she’s a female Indiana Jones-slash-Ninja. Just because.
That character is pretty much a Mary Sue. She’s perfect in pretty much every way. Her adventures are goddamn boring. The entire point is to go “Ooh! Ahh!” over her revealing costume and her amazing unstoppableness. Of course, she has a sensitive side but that doesn’t stop her in any way. Seriously, Sean Bean stole that movie because there was nobody else in it.
So, the issue is that female characters are often unrealistically strong in a setting which doesn’t support it. I have no problem with a mighty female superhero in a superheroic setting. I have no problem with a badass female hero in a setting which gives them plausible limitations and personality. Ripley is human: she wants to go home. She wants nothing more than to leave this nightmare. Her strength comes form the fact that doesn’t give into despair and knows she’s not some unstoppable badass.
I think you’d also find a lot of cheezy amusement in the male badasses. It’s possible to enjoy Lara Croft as a popcorn flick. But that doesn’t make her a good character, just looking at her as a bad copy of a 1980’s action hero, with girly bits.