To elaborate on my first post, I tweak classes and use new base classes for two reasons. First, I generally dislike the use of the multiclass rules and use of PrCs for handing concepts (cultural, literary, and occupational) that can easily be explained by initial training and are both viable for a first level character and setting appropriate. Second, I prefer classes to be the result of months or years of training (formal or informal) and, therefore, not something that should be switched easily.
From my perspective, the multiclassing rules, as written, feel like one is focusing upon one class at a given time upon leveling. If you are a multiclassed fighter/wizard, you might get good BAB, d10 hp, and have one set of skills as class skils one levels, but the next level you get poor BAB, d4 hp and another set of skills as class skills. While hd, bab, and number of skill points average out, the approach creates a feel that one is focusing on one class or another at a given time. Imo, this is fine to reflect someone trying to pick up a new class or put all their focus into one class at a given time. However, again imo, when the multiclass rules are applied to someone whose initial training combined aspects of two classes (e.g., fighter/wizard or cleric/monk) and whose development focuses equally on both classes from level to level, the development at each level has a schizophrenic feel rather than that of a unified concept. A class variant such as the battle sorcerer or new base class such as AEG's Myrmidon removes the schizophrenic development pattern as the Hit die, BAB, class skills, etc. remain consistant from level to level as with any other class,while still retaining the slower development in fighting prowess than a dedicated fighter and slower access to higher spell slots than a dedicated spellcaster
With regards to prestige classes, I think they are perfect to represent an elite order within a culture (e.g., the Glessian Berserkers, the High Druids of Valinor) or even advanced focused training. However, there are many prc concepts that are viable for beginning characters. In some instance, these concepts are simply a reflection of initial training. Sometimes the training simply reflects a deviance from the standard first level class features (e.g, class skills, starting weapons, etc.). In other instances, the concept is a a blend of two classes (e.g. Swashbuckler, Scout, Warrior mage, divine monk). Regardless, if the concept fits an archetype (cultural, literary, professional or setting specific), is viable for my setting, and is reasonable for a first level character, I prefer a class variant or new base class that makes the class viable at first level- I don't see the reason to have the player jump through hoops when it is not necessary.