The approach I use is to choose the majors and minors carefully for the character I think I'm building, and then just try and balance out when a level is almost due. Provided you haven't made all your heavily-used skills majors, you'll have a good idea when you're close to a new level, and will be able to top up a minor or two by repairing things before you sell them, or haggling harder, or getting some training instead of buying that extra house. I don't panic about "wasted levels" in other skills, as you can't easily avoid using more than 9 skills during a level - that's three attributes to get +5 times the three skills that contribute to each.
Also treat 5/5/5 as a goal, rather than a "must complete". Expect to miss most of the time and settle for 4/4/3. But do have a plan to avoid 2/2/2 or you'll be dead all the time.
This is how I set up my custom class:
Major
Armorer, Hand to Hand, Illusion, Mysticism, Restoration, Light Armor, Marksman
Minor
Athletics, Blade, Block, Blunt, Heavy Armor, Alchemy, Alteration
Conjuration, Destruction, Acrobatics, Mercantile, Security, Sneak
Speechcraft
All of the major skill can be controlled. Athletics can even be controlled with the use of a horse. However, athletics levels rapidly early and should be taken advantage of in conjunction with light armor (if desired) for the early speed boost (+5). Still, you haven't answered my question. How much control is really required? Attempting strict control makes the game both a pain and no fun. I'm trying to gain a balance between playing and efficient leveling to maximize a character for an actual 20+ campaign. Otherwise, the whole game -with KOTN and Shivering Isles - can be completed before level 10 end the gamer never enjoys the best leveled gear.