I struggled the first time I played with Abilities and how--well, they are sort of open ended and vague. I ended up using Athletics for pretty much everything. 

So I came up with a rules tweak.

If I just made the players start with three base Abilities: Physical stuff, Social Stuff, Mental stuff which they could use for any act, but take one penalty dice, would this work?

What problems would I have if I tweaked the rules this way? I'd probably have to switch the pools to those categories as well.

The rules are intented to work just as you played them - you can use most Abilities for most situations, especially when you adventure in situations that correspond with the Ability. In other words: if you're a carpenter, all problems look like nails. You can use your Athletics as much as you can stand to, and don't let any freeformer tell you otherwise - it's not a sin to have an useful Ability. And if you find yourself using your Athletics in situations where you don't feel good for using it - why are you doing it, then?

Interestingly enough, I give your rules tweak in the Finnish version of the game: if a player wants "attributes" like you'd have in a trad adventure rpg, that's the way you do it: give the character some vague general description like "Strong" or "Smart", which is defined as a generic Ability, mostly useful as a support for other Abilities. Perhaps could use them for tasks that require no special skills, but at penalty due to difficulty.

So yeah, that's not so far out. I wouldn't switch the Pools around for this kind of minor stuff, though - rather, just go into the game with the idea that you'll be using generic, attribute-like Abilities. The game is intented to work with player-defined Abilities, so you'd better get used to not having perfect symmetry and GM-guaranteed balance to your Ability list - an important part of character definition is having only the Abilities that are significant for that character.

Thus, instead of changing the rules, try the following the next time you create a character: give your character some (not all) of the following abilities as well as the more typical ones from the book. That should give you enough of a traditional grounding to feel comfortable with the system. And it's pretty fun, too. I could well imagine making a "Tarzan" type character who only had these at the start; a very well-rounded guy, but not exactly capable of anything special.

Strong (Vigor)
The character is exceptionally strong. This Ability is useful in a vide variety of situations in a preindustrial setting, beginning with farm work and ending with prodigious feats of strength. It is, however, primarily suitable as a support Ability for an Ability specifically suited to a physical task; using it alone for any complex craft or task is grounds for SG penalty dice.

Nimble (Instinct)
The character is exceptionally agile and dextrous. The Ability is useful for any physical tasks with gymnastic elements or requiring coordination, such as athletics or dancing. It is, however, primarily suitable as a support Ability for an Ability specifically suited to a physical task; using it alone for any complex craft or task is grounds for SG penalty dice.

Endure (Vigor)
This is your character's ability to push on and persevere though pain and fatigue. It is used to test the limits of a character's physicality and fitness. It is, however, a passive Ability that is primarily suitable as a support Ability for an Ability specifically suited to a physical task; it can only be used alone to ignore inconveniences, not to do anything active.

Smart (Reason)
The character is exceptionally smart. The Ability can be used in pretty much any situation requiring learning, knowledge of simple thinking. It is, however, primarily suitable as a support Ability for an Ability specifically suited to an intellectual task; using it alone for any research requiring special knowledge is grounds for SG penalty dice.

Wise (Reason)
The character is exceptionally wise. The Ability governs the character's moral compass, life experience and perceptiveness in human affairs, making it useful for detecting the truth, resisting temptation and other such situations. It is, however, primarily suitable as a support Ability for an Ability specifically suited to a human situation; using it alone in a social situation is grounds for SG penalty dice.

Amiable (Instinct)
The character is exceptionally charismatic. The Ability is used to get other people to like the character in general, and for any follow-up situations among friends and allies. It is, however, primarily suitable as a support Ability for an Ability specifically suited to a social task; using it alone in a situation requiring specific approach or manners is grounds for SG penalty dice.