The standard Eberron model of APs won't cause a major change in the game. Using the far, far more liberal options from Unearthed Arcana, which include regaining just cast spells, using a feat you don't have (which, given Epic feats....), an extra action (move and full attack....), and even, if memory serves, casting a spell using a metamagic feat 'on the fly' (ie, Suddenly), will drastically change the game.
The Shackled City game I'm in has gotten through the first two adventures with minimal difficulty. We had trouble with the climax of the second adventure, simply because we were not prepared. But we surivived running away, came back, and wiped the floor with the opposition. Use of the action points, even at low levels with fewer options, has made the difference on many occasions.
Players have another powerful set of options at their disposal. The limited number of action points simply means they only use them when needed for maximum effect. And the effects, especially at epic levels, can be really incredible. What I would actually recommend, given the 'in game' reason you mentioned above, is to allow in game methods of gaining the use of some of the options. A given character may gain the ability to use Action points for options A,B and C; a second character gets B,D and E, a third gets A, F and G, etc. This allows you to tightly control what options which characters get - and if all goes well, can create ways to allow the characters to grow their list of AP options. And if things get interesting in a bad way, you can have abilities fade away, or simply not increase.