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The term 'Mary Sue' is bandied about too much these days. The three Companions we've had so far - Rose, Martha and Donna - actually represent three different types. Rose was originally a type of the standard classic Companion - screaming, asking pointless questions, etc. In this regard, she's much like Jo, Victoria or Tegan. But as the series progressed, she started to mean more to the Doctor, a la Sam Jones, Grace or Sarah Jane (I'll get to that in a moment).

Martha was more in the way of New Adventures/Eighth Doctor Adventures mold : a strong, independent woman who, in the end, decided that her path didn't involve traveling with the Doctor. In this way she's more like Benny or Anji.

Donna is, like Romana II or Ace, somewhat unique. She's the first Companion to actively seek out the Doctor, and even stands almost as an equal. In fact, she's the key element of Series 4.

As I've said, Sarah Jane Smith stands apart from all the others save Rose. The producers originally meant for something between SJS and the Doc, but felt that that might be too much for a 'children's show'. Just look at the way they acted - in several episodes it's obvious he doesn't want her to leave (The Android Invasion and Terror of the Zygons stand out.). Further, look at the comments Mickey makes during School Reunion - at no point does the Doctor dispute his allegations.

But more than that, all companions are meant to be Mary Sue's to a degree. I mean, c'mon, a normal person getting the chance to whiz through Time and Space? Dream come true! 'Mary Sue' was a term coined to reflect a trend in Star Trek fanfic - and a pretty silly one at that. Hope this helps.

So you think all characters are Mary Sues? That doesn't make any sense. A Mary Sue is an extreme, over-the-top type of character. You can't have someone that's "a little bit of a Sue" or "a Sue to certain degree". They're either a Sue or they're not. Like I said before, every character has some "Sue" aspect(s) to them. What makes a character a Sue is having too many of those traits AND being written in an annoying way (such as the author constantly going on about how great the character is in the narrative or in other characters' dialogue as an example).

You know what... just read the wiki. Especially the criticism part at the end.