I prefer the class system as is, for several reasons:
- I find that it helps in role-play, as my character's class informs some key components of her background, skill set, tactical choices, etc. If the character is, for example, a war hero or sole survivor, her class gives me a sense of how she accomplished those feats - and ultimately gives me a stronger basis for character definition.
- It provides a structure for replayability. Trying a different class in a new playthrough would provide a very different character / background / experience.
- Squadmates are typically built per some sort of class template, and typically have a character-specific unique ability to differentiate them. Taking away those base templates could make squadmate design and selection much more complex, and more difficult to balance.
- It could limit level, battle, and enemy design. I'm still not happy about the fact that the same abilities (overload, disruptor ammo) were changed to be effective against both shields and barriers in ME3. It homogenized them, and made the difference between shields and barriers meaningless. I'd like party composition to matter, and to have some enemies / battles where not having the right abilities would seriously affect your ability to succeed. Allowing cafeteria style skill selection (a classless system) would discourage the development of unique enemies with unique abilities and defenses, because the designers would need to be sensitive to and aware of all of the different possible skill combinations the player might choose.