Suggestions: Rather than have squares expand to fill the cell representing a skill, a left-to-right sweep would be nicer. It's hard to notice if a Dwarf has a tiny pixel of skill or not (especially on Group By Profession where you can't sort by skill), plus it provides better precision in judging which Dwarf is more skilled as you get twice as many pixels.
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It sounds like your issue is identification of low-skilled dorfs and differentiating between closely-skilled dorfs.
Couple of things to try in the short term: Try re-sizing the cell size (options, cell-size) a pixel or two to see if the low-skills show up better for you. Also make sure you turn on "auto-contrast skill display" to make sure the fill color is inverse from the background.
With respect to the differentiating between small differences (e.g. skill=5 vs 6) I am not sure this would appreciably change by going to an X or Y scale since there are 15 levels to distinguish and we're talking about a default 17x17 pixel size. There are generally two ways to deal with this, the simplest being object distinction which means either changing the shape or color as the levels progress - replacing the incremental fill with the number value of the level, for example.
The other way is through series distinction - think of the stick counter for the number 5, four lines with a fifth line drawn through to easily distinguish groups of 5 in the series. This latter design can come in all kinds of forms; the money bags vs. coins in Civilization comes immediately to mind, but off the top of my head i have no ideas how this might be represented in DT, but mod is the programmer so he has a better sense of what would be possible in this regard.
Pardon the ramble....in any case, hopefully resizing the cells will help you while mod considers your request.
Poking around the ini files, I need to make a view that separates Necessary/Useful/Semi-Useful/Useless skills by group.
You don't need to poke around in the .ini's at all - you can make your own custom views/sets and create the display any way you want, with as many views/tabs as you want !!
See my earlier post - i posted a screencasts showing how to do thisEDIT:
Making your own views and sets from scratch:
http://screencast.com/t/UoW2MEVF Cheers