The best way I've seen it done is that the novice and higher feats grant you more uses of the initial feats power.
So a fighter multiclass gets mark and +1 attack once per encounter, with notive he might have it 2 times per encounter, and so forth. Even that would be very strong, but it would be less extreme.
Unless someone else happened on the same idea, that was mine. It was a bit strong, and didn't scale very well. I started on an idea to give additional, specific class features as you got one two and three power swap feats. Had trouble with fleshing it out though, as the nature and power of class abilities are rather inconsistent. My Dual Class and Paragon Path ideas went out the window with the rewrite, as well.
Might as well share what I came up with. Can't quite say how balanced it is, but it looks good to me, for what it's worth. (Although that's probably not much

)
Initiate of the Faith [Multiclass Cleric]
Requires Wis 13, Religion skill
Grants Healing Word 1/day, use Holy Symbols as implements
Power Swap 1: -
Power Swap 2: Healers Lore 1/enc
Power Swap 3: Channel Divinity 1/day
Student of the Sword [Multiclass Fighter]
Requires Str 13, Any Military weapon proficiency
Grants Mark 1/enc
Power Swap 1: Combat Challenge (interrupt marked enemy) 1/enc
Power Swap 2: Combat Superiority 1/enc
Power Swap 3: +1 with one or two handed weapons 1/enc
Soldier of the Faith [Multiclass Paladin]
Requires Str 13 and Cha 13, Religion skill
Grants Divine Challange 1/enc, Can use Holy Symbols and Holy Avengers as implements
Power Swap 1: -
Power Swap 2: Lay on Hands 1/day
Power Swap 3: Channel Divinity 1/day
Warrior of the Wild [Multiclass Ranger]
Choose either Two Blade or Archery fighting styles
Requires Str 13 (Two-Blade) or Dex 13 (Archery), Dungeoneering or Nature skills
Grants Hunter Quarry 1/enc, Qualify for Paragon Paths requiring Two Blade or Archery fighting styles
Power Swap 1: -
Power Swap 2: Twin Strike 1/enc
Power Swap 3: Use one handed weapons as off hand (Two-Blade) or Prime Shot (Archery)
Sneak of Shadows [Multiclass Rogue]
Requires Dex 13, Thievery skill
Grants Sneak attack 1/enc
Power Swap 1: Rogue Weapon Talent 1/enc
Power Swap 2: First Strike 1/day
Power Swap 3: Artful Dodger or Brutal Scoundrel 1/enc (choose only one option) (apply to either it's normal effect or power bonus)
Pact Initiate [Multiclass Warlock]
Choose Fey, Infernal, or Star pact
Requires Int 13, Con 13 (Infernal) or Cha 13 (Fey, Star)
Grant Pacts At-will power or Eldritch Blast 1/enc, use Rods, Wands, and Pact Blades as implements
Power Swap 1: Shadow Walk 1/enc
Power Swap 2: Warlocks Curse 1/encounter (Lasts for entire encounter, but only get damage once)
Power Swap 3: Pact boon from cursed target 1/enc
Student of Battle [Multiclass Warlord]
Requires Str 13, Int 13 (Tactical) or Cha 13 (Inspiring)
Grants Inspiring Word 1/day
Power Swap 1: -
Power Swap 2: Combat Leader 1/day
Power Swap 3: Inspiring Presence or Tactical Presence 1/enc (apply to either it's normal effect or power bonus)
Arcane Initiate [Multiclass Wizard]
Requires Int 13, Arcana skill
Grant one wizard At-will power 1/enc, use Rods, Wands and Orbs as implements
Power Swap 1: Spellbook
Power Swap 2: One cantrip, usable at-will
Power Swap 3: Arcane Implement Mastery (special effect 1/day)