The 55/3.5 Micro-Nikkor is better than the 55/2.8, I think. How about the 200/4, which seems to get overlooked a lot?
the 200/4 ED IF is a nice lens but in reality it's not in the top pack of macros anymore, though I suppose at it's focal length there isn't much competition. Canon 180/3.5 macro? yeah, I think that's about it. the manual 200/4 isnt as good as that.
the 55/3.5 IS better than the 55/2.8. In fact, if there is one lens who's reputation is as undeserved as the 55/2.8, please let me know. Consider it's measured MTF graph:
how that much field curvature at f8 is acceptable in a macro lens is beyond me. that is awful, no two ways about it, if you consider what sort of stuff a 55 macro would be expected to do (ie copy work).
let's consider Pentax's try:
the 55/3.5 Micro Nikkor has a flatter field and is an actually good short macro. how about one more? try the Zeiss 50/1.4, but recall that 50/1.4 lenses just have field curvature as a result of the the challenge of their design:
MTFs rarely matter. unless we're talking macros. where a flat field of high contrast reproduction is what youre buying. it's not that the 55/2.8 is a "bad" lens per se, in that it is sharp. but it fails it's purpose, which should be the main consideration.
ps these are bench MTFs of the lens, not the system, making them directly comparable.