I think the biggest problem with people who argue against d20 is that they think of D&D and fantasy-specific elements rather than the game mechanic. The mechanic is: roll d20, add bonuses based on ability score and skill rank, compare to minimum success level (DC). Hit points are an abstraction for luck and toughness, and one can replace that component with a grittier system (although I've heard a lot of arguments that hit points are appropriate for Trek). d20 is no better or worse than a pool of d6.
Another major problem with people who don't even look at the system and try to argue against it is that they (illogically) try to tie level to rank. LEVEL <> RANK! A lieutenant going on away missions could have lots of talent in some area (suggesting high level and skill focus) while a captain could have knowledge of a wide range of things (suggesting nothing about level, just that he spread his skill points across many fields). Think of the captain as a manager. I work for a person who is a starting rank in my company, but he's older and pretty good at discipline and motivation of workers. His "rank" is minimal (equiv to LT) but he's one of the best managers and technical contributors in our group. In contrast, the top of the food chain here is a higher "rank" than his manager, according to the title and grade scale of the company, and he definitely has more skill (even managerial) in the fields the two of them are in than his manager. That guy is equiv to a Commodore while his boss is just a Captain. I'm just trying to show that greater skill (and thus level) does not mean greater rank and that higher up the command chain does not mean higher rank or skill.
There's absolutely nothing wrong with a captain with only 3 levels in d20, or a lieutenant with 13 levels, or said LT reporting to said CPT. A character in ICON/CODA can gain a lot of skills and edges but not be a captain if he hasn't bought "promotion" edges. So d20 is no different from ICON/CODA. But instead of getting a skill point at a time, you get them in surges (say 6 or 8 skill points at a time) and call it a level. Silverstreak said, "D20 is level based, ICON and Coda are skill based." That's a horrible misunderstanding of the purpose and terms of level and skill. Skills are not a comparative factor to levels, they can be compared with classes. d20 is class-based, but if you only have one class, it becomes skill based.