Firstly, since I am a huge fan of AE, I would start with the 13 classes from that system, and then work back toward a more vanilla middle ground. One of the biggest complaints people have about AE is that many of the classes are too mystical or have too much flavor baggage, so I would just take the classes that are tried and true vanilla fantasy archetypes, the Champion (warrior of a greater cause), the Mageblade (fighter-mage), Magister (wizard), Unfettered (swashbuckler) and Warmain (heavy armored warrior).
Without the Akashic and Totem Warrior, our list lacks skillful and nature-oriented characters, so let's take the Rogue, Ranger, and Barbarian from 3.5 to address that issue, since they are all solid classes mechanically, and are instantly recognizable archetypes. In order to make these fit with AE, we replace the Rogue's trapfinding exclusivity with the ability to get a free check to notice secret doors or traps within 5ft, much like the elven racial ability, make Improved Evasion a mandatory choice for the first rogue special ability, and replace all the other special abilities with bonus feat slots (since in AE, all the others are feats anyone can take). As for the Ranger, we can take the Complete Champion variant as a model and give them bonus feats instead of spells, importing ranger specific feats like Improved Favored Enemy where necessary.
Now our list only lacks for three archetypes from the core set, the Bard, the Cleric, and the Druid. Since I have the Book of Eldritch Might, the first one is easy, I simply drop the variant Bard class from that book, including it's spellnote casting system into the mix. As for the latter, at this point I break out the homebrewing skills. The Greenbond is a solid primary caster with a focus on healing magic that was only cut for flavor reasons, so let's bring that back, reflavor the special abilities and skill list to be more divine and less plant-oriented, and call it a cleric. The free Ptolus/AE conversion document does most of the work of getting our cleric domains into the AE casting system, although my preference would be to make a feat called "Cleric Domain" that only the cleric can take. As for the Druid, let's take the Shapeshifting variant out of PHB2, reduce the fort save to a medium progression (like our greenbond/cleric), and give it the witch's spellcasting progression with improved access to any spell with the Animal (Litorian and Sibeccai, with a few exceptions) and Plant descriptors. Since there's a lot more incentive to remain in animal form at this point, let's throw in the Touch of Vitality ability from the Dragon Shaman, and specify that unlike their spellcasting, it can be used in animal form for a bit of combat healing. Alternatively, you could skip the work and just look at the final product on my wiki, here:
Cleric
volkheim wiki / Cleric
Druid
volkheim wiki / Druid
So after all that, we come to our final list of eleven base classes:
Barbarian (PHB)
Bard (Complete Book of Eldritch Might variant)
Champion (AE)
Cleric (AE Greenbond variant)
Druid (PHB2/AE homebrew)
Mageblade (AE)
Magister (AE)
Ranger (PHB with Complete Champion variant)
Rogue (PHB with houserules)
Unfettered (AE)
Warmain (AE)