That's certainly a consideration, but I'd say that has an awful lot to do with the positions they played. There are fewer third basemen in the Hall of Fame than any other position, and the careers of most catchers are usually so short that the offensive numbers of even the good ones are often borderline marginal.
Gwynn wasn't one of the best outfielders of all time for one simple reason: there are tons of great ones in almost every era -- including (arguably) six of the ten greatest players of all-time: Babe Ruth, Ty Cobb, Willie Mays, Joe DiMaggio, Hank Aaron, and Ted Williams. Tell me how well the sixth-best catcher or sixth-best third baseman of all time stack up against those guys!
Lack of both power and speed mark Tony down for an outfielder.
He definitely didn't have much power, but he was not a slow man until the end of his career (much like Babe Ruth, when you think about it). He won five Gold Gloves and stole 319 bases in his career -- which is three more Gold Gloves and about 120 stolen bases than the "immortal" Pete Rose had in a longer career (he also hit 35 points higher than Rose for his career, for what that's worth).
Gwynn's only real problem was that he spent his entire career in San Diego.
You're right. I stand corrected. I didn't realize Gwynn had stolen that many bases. I had forgotten that in his early years Tony was quite a base stealer--56 one year and 40 another!
BTW, he wasn't totally without power--135 HR. And his .459 SLG is not too shabby. Still, I wouldn't rank him in my top dozen OF of all time, maybe not the top 15 or 20.
As to Rose, I am not one who thinks of him as "immortal." Even apart from his off-the-field problems, I would not put him in the top 15-20 at any of his several positions.