Hmmmmm. It seems to me that in only a few instances you would use a 'simple ability check' vs a full blown 'skill check'. Not because it is inherently wrong, but because it is confusing (at least to me). There needs to be some justification for NOT just using the skill check. If the only justification is that you don't want it to be too easy, I would suggest increasing the DC (however I do understand that when you get higher level characters the DC may have to be ridiculous when you start adding ability, skill, level, and perhaps an additional modifier, but is that really the case? I suspect a 30 DC is going to be tough for even higher level characters.).
However... there are some instances when a simple ability check is more appropriate. So if the action is more or less a Will Save, I could see how a simple MIND check would be clearer and appropriately more difficult. How about saving for poison? STR. Dodging a trap? DEX. But even with these examples perhaps a skill check would be better or at least no worse? How did you do the Will Save? Could a skill be used in combination? How about the poison, was there knowledge of an antidote that helped reduce the effects? Even dodging a trap could involve physical, subterfuge, or knowledge. And of course increasing the DC when you add the level and the skill.
Part of the fun of Microlite20, IMHO, is that you get to improvise what the Skill Check involves, and how the Character actually does it. There is no one right way of doing any skill check.
Again there is nothing wrong with using a simple ability check vs a skill check (and in fact there are situations where it makes a lot of sense), but I do ask why? How is it better than just using the standard mechanic of the game? In the absence of a reason I would avoid it. Life is complicated enough, why make it more so? I have a hard enough time remembering the rules to my own games I have written.