Halo: Combat Evolved was innovative. Halo 2 and Halo 3 built upon and refined those innovations. There were a number of subtle, yet cleverly implemented mechanics, some had already been seen before in similar form, but nowhere had they been brought together so expertly as Halo: Combat Evolved, or in its sequals. I also found it a refrehing change from the Half-Life formula, which every story-driven action adventure game seemed to be adopting at the time. Here is a quick list of innovations off the top of my head:
(1) The rechargable shields, both on the Master Chief and some opponents. This simple system diffused a common problem in similar games; namely, surviving a confrontation with barely any health, and then proceeding to the next confrontation with little or no chance of success. The rechargable shields guarunteed at least a minimal level of health for each confrontation, and enough to pass any of them. There were also many interesting strategic options opened up by this mechanic, both defensively and offensively. For example, chasing down an Elite before he can take cover and recharge his shields.
(2) The two weapon limit. This solved one problem and opened a new level of strategy. Regarding the former, it solved the problem of navigating through a menu to select from a dozen weapons, which is a particular nuisance on the consoles with control pad. Regarding the latter, it opened the way for tactical decisions, such as deciding which weapons to carry into battle, and how best to make use of the weapons which you have. I think this contributes someway to the "never the same fight twice" effect which many experience with the Halo series.
(3) Overheating Covenent weaponary. In the Halo series the Covenent weapons rarely need reloading, rather, they have a set charge to use before being disposed of. This means that they are absent the standard problem of reloading, which usually injects a subtle layer of strategy to confrontations. This is compensated for by overheating, which provides a similar deficit to reloading, but with its own unique quirks. The same mechanic has reappeared many times since where weaponary does not need reloading, most recently in Bioware's Mass Effect.
(4) Melee attacks as a useful alternative. Chalk this up to my bad memory or lack of experience, but I do not remember melee attacks being the same before Halo: Combat Evovled. They were something you used at the beginning, often before acquiring a proper weapon, and were pathetically weak against stronger opponents. Throughout the Halo series, melee attacks were interesting and powerful alternatives, and in the right context would open up new tactical choices.
Half, if not all, of these innovations have made it into subsequent games, such that they seem to have been taken for granted. The main exception is Half-Life 2, which seems to have ignored the pack entirely. I should note, I do not consider this a bad thing, since I like the variation and Half-Life 2 is one of my favourites, but I just think it is mistaken to say that the Halo series is generic and unoriginal. There is plenty of innovation and refinement to be found, and its influence can be felt on almost every release since.