The things that are not included under the SRD are character creation and level-up rules, and then most of the mutant creatures TSR and Wizards have invented over the years, like mind flayers, owlbears, and beholders. For the most part, these little omissions have been circumvented by people putting out new games, with renamed creatures almost-like the ones that were omitted, and brand new character creation and leveling rules. In some cases, the replacement rules are actually an improvement, like in Pathfinder.
Where it FailsWhere the SRD falls painfully short is the extension of the license to where people can use the SRD to publish interactive games, MMOs, and other new ways to play the game. Pathfinder's MMO (in development) needs to rewrite an entire new rules system to use for the online version of the game. The SRD limits a game designer who wants to write a game that has an entirely new way of playing it, like via tablets with people around the world online. This one point I think is the greatest failing of the license, and the game you design using the SRD isn't entirely yours.
This makes the OGL/SRD combo different than the Linux license in a very specific way. With Linux, the code can be modified as long as it is licensed for others to use freely and in new ways (I am speaking really generally here, Linux fans). With the OGL/SRD combo, the game can't be used for online games, social networking games, or for any truly new and different way of playing. The OGL/SRD limits you to a book, table, and dice. In a way, it holds back the art and design of new RPGs - ones we have no idea how they will be played.
I Love My Games, But as a Designer...I love playing my OGL/SRD games, mind you, I love 13th Age, Pathfinder, Labyrinth Lord, and all the other wonderful creations built under the combo. A part of me is sad though, knowing these games will never advance the art of game design beyond the d20 clones, and never be played in new ways. As a game designer, you want to work without limits. A huge part of adopting the SRD is a limit, and I wonder if new games should just take the public-domain parts of the D&D lore, and establish something truly free and new, without restrictions, and break from the SRD's chains.
This has to be one of the most difficult pieces of the hobby for me to deal with as a game designer. The OGL/SRD combo is an incredible resource, but using it could be holding back the art of RPG design. Mind you, some companies could care less about the OGL/SRD combo, like Fantasy Flight Games and others, and are creating new experiences with these games. How open these efforts are is always an issue, and the OGL/SRD is the defacto standard for D&D-like experiences.
For free and open gaming, there needs to be open standards a community can agree upon, public domain legends to pull from, and a license permitting remixes and new ways on playing the game people may have never envisioned. The only real way out is to design your own rules system, as the SRD is a limit in regards to game design and what you can do with your game.