Comparison: Feat 'n Skills Mage versus the standard sorcerer
(I'm using 3.0 because I haven't bought 3.5, if that matters)
I'll use the standard ability score array, but maximize it differently:
Sorc: str 8, dex 14, con 13, int 10, wis 12 cha 15.
Mage: str 8, dex 10, con 13, int 15, wis 12, cha 14.
Let's assume that both are human to maximize feat potential.
First Level:
Sorc: 5 hp. +0 BAB. Has 12 skill points (spellcraft 4, other skills 8). Has 2 feats that can be used for anything. Knows 4 cantrips (mage hand, flare, light, resistance) and 2 first level spells (for damage, magic missile and sleep). Capabilities: 1d4+1 magic missile (no save) cast up to 4 times per day. Can also sleep, do minor telekinesis, and give small bonuses and minuses.
Mage: 7 VP, +0 BAB. Has 40 skill points: for maximum flexibility, this mage uses all but 8 skill points to max out 7 magical skills plus arcane awareness. 3 feats: arcane ability, conjuration (for flexible damage, although one of the evocation skills would do just as well), enchantment. Magical skills: creation (+6), forces (+6), travel (+6), compel (+6), emotion (+6), curses (+6), charm (+6). Capabilities: forces: can lift up to 175 lbs. a short way (3 VP); do 3d6 damage with one spell (spell roll 11, save DC 16), then rest for 7 hours; or do 1d6 damage (spell roll 8, 3 VP each) twice before resting. Most enchantments will have a save of DC 15 (for one powerful spell) or less. After such casting, the mage will be at 1 vitality point, being more vulnerable in combat.
The first level mage is much more flexible, and (within certain limits) much more powerful (especially if material components are used). Total damage capability edges slightly to the sorc., especially if saves are taken into account.
6th level
Sorc: Average 23 hp. +3 BAB. Has total 18 skill points. Now knows fireball (5d6 dam. save DC 16), casting 4 times per day. Can also cast magic missile 7 times per day (7d4+7, no save) and Melf's acid arrow 6 times (total 12d4 dam., no save). Has great flexibility in spell selection, but will still be rather narrow in capabilities (only 2 second level spells known).
Mage: Average 30 VP, +0 BAB. Has 93 total skill points after increasing intelligence at 4th level. If the mage maxes out on skills taken at beginning and takes school specialization and 3 skill focuses in conjuration, the conjuration skills are now at +15 (with increased save DCs), and the enchantment skills are at +11. Forces could now be used to 5d6 force damage (spell roll DC 22, save DC 20, VP 11, takes 3 rounds to cast safely) against one target. To get the 20 ft. radius that the fireball has, the mage would be reduced to 1d6 damage over that radius. If an inexpensive material component is used, the mage can cast this three times before needing to rest for 5 hours (so potentially 9 times over the course of a day if the enemies conveniently arrive far enough apart, but 4 is probably a more likely number). The mage is also quite good at charms, curses, and other such things, and is even able to teleport somewhat safely now.
So, the sorcerer is still somewhat better at widespread damage dealing, but the mage is more flexible. Keep in mind that if the mage actually kills people, he or she will be forced to try corruption checks. Also keep in mind that anyone with arcane awareness high enough or close enough will be aware of the mage (which may not be a good thing).
Beyond that, the comparisons get even stranger to make. Overall, the mage is much more flexible, but can't cast as many spell as often. The mage is forced to make spell rolls, but can generally create much higher save DCs as well (although the sorc has several no-save damage spells). The flexibility-within-limits of the spell skills versus the grab-bag approach of the Vancian system makes a mechanical conversion system difficult; the only advice I would give is to focus on the most commonly used spells and find a skill that produces a similar effect. In earlier incarnations I tried to mimic the power level of the standard system, but eventually gave up.
Does that help?