IE Link may have a disjointed hitboxes however he doesn't have a backup plan against ike, marth, olimar, or pit. They all have the backup plans of better priority, fair rush, easily spammable projectiles, and easily spammable projectiles with great recovery respectively.
I don't really see where you're coming from here. I find that Link stands up pretty favorably to Ike, Marth, and Pit.
Ike can be easily controlled by projectiles, as he has no real answer to them and is way too slow to just rush through them. You can force him to make unfavorable approaches and then punish his lag.
Projectiles are similarly helpful against Marth, though since Marth is much faster (and better in general), it's not as drastic. Link doesn't have a range or priority advantage anymore, but he still partially cancels out Marth's, and that's almost as good. I'm sure it's still not
even, but it's a good fight, and Link holds up quite well considering that Marth is way up there on the tiers. It sure as hell doesn't feel like one of the best character beating mercilessly on the worst character, that's for sure. Also, when Marth is recovering, Link can sometimes do this:
http://www.youtube.com/watch?v=zKNH03XT0J8 (2:25 especially). And that's just hilarious.
With Pit, you do have the problem of the arrows preventing effective use of Link's bow or boomerang. But it's not exactly hard for Link (or anybody) to advance through Pit's arrows (dash, powershield, repeat), and once you're in close combat, Link has a significant range advantage over Pit's toothpicks.
I don't fight against too many Olimars (or against Links as Olimar), but Link probably does have the disadvantage there. He's obviously going to have some bad matchups. It's not like I'm trying to put him in the high tier, here...I'm just saying he's not bad enough to be at the absolute bottom.
The point is that these are mostly upper-tier characters, and Link has the tools to handle a lot of them. Maybe not enough to be called a counterpick or anything, and definitely not to the point where he's a superior character in general, but enough to be viable. More viable than I would expect from the bottom tier.