Zegapain

Both deals with alien invasion and (near) destruction of mankind. Both are equally depressing but have a very solid plot and character developments. Soundtracks are great too. 

Both are sci-fi with lots of mecha battles and very similar in their conflicts on what is reality and what is not. Rahxephon has enclosed spaces separate from the outside world where people live oblivious to the actual situation outside of these zones, in which humankind is battling the enemy. They are similar in appearance to the Deutera areas but conceptually like the quantum servers in Zegapain. Also in both anime the enemy appear human though they are not. The main character is in both cases a male and have a love interest. 

Another good storyline with meca action, Characters are well developed with a ever changing storyline and aftermath affects of that on the characters themselfs, worth checking out. 

You can sense the influence of Neon Genesis Evangelion into Zegapain. Both animes are not just about an ongoing war against a higher being, and are heavily focused on the psychological state of the protagonist. Zega suffers from the early digital animation era but its direction and scene compositions give the anime a mysterious and introspective vibe just like Eva. 

They are both anime in which a naive protagonist is forced to face reality and fight in giant mecha -giant mecha -mecha battles -similar background stories -amazing characters This is the show for that little corner of your head that is secretly wanting you to spend the entire night watching this mech fest of awesomeness. 

both are mecha shows about a digital world in which the protagonist has lost his previous memories.  

without being able to spoil it: the world is similar in some way the rest on the other hand is pretty different: ranging from characters, to story to structure. 

Both Sword art Online and Zegapain are action / romance anime, without (too much) harem antics or Ecchi. Though zegapain deals with more complex issues, if you like one chances are you'll like the other  

Both of these anime focus on an odd futuristic setting where mechas are used to solve the plot issue. One big tie these two have is the romantic role within the story. Both have mecha fights and sort of political wars while developing the romance between the two love interests. As the story moves forward the romance builds up. The only difference is that Blue Drop is much more tragic than Zegapain 

-Both blur the line between digital data and real life--- specifically the idea that people can be transferred as data into the net. -More importantly, both use this trope to talk about dealing with the loss of loved ones and moving on.  

Both feature plots where the main characters pilot robots in what they assume is a game, but as the plot goes along they start to question their circumstances 

Both works - mecha anime with cyberpunk elements. Both slightly similar to the "Matrix" movie: MC learns the true about nature surrounding reality world. 

Both animes takes place in a parallel world where the protaganist has to pilot a mecha to fight in order to get themselves back to the real world they believes in. 

Both are cyber-mecha series that deal with two parallel worlds. One cyber, one real. A conflict in one world, eventually affects the other. 

If you like a good story with meca involved then zegapain is the way to go. Its got a very good ongoing storyline with many twists. The meca designs and concepts are very unique in zegapain. So go find and enjoy! 

Both anime make in depth reference to quantum mechanics, and carries the many themes associated with it such as, identity, reality, conscience, etc. While Zegapain appears more directed at action and Noein attempt to explore these themes are the further level, both are appropriate animes if you are into sci fi animes that’s more than just giant robots flying around shooting lasers. 

They're similar in their post apocalyptical settings, and their way of kind of salvaging the human race; although zegapain has a much more drawn out story line but both equally entertaining. However, zegapain also has a better transition than interlude does in terms of realizing what is actually happen.  

Matrix style series and a whole new world on the other side. 'Zegapain' isn't solid in terms of storyline but you are able to connect with a few of the characters and in the beginning, it's pretty much hack and slash in mechs but halfway through the series, more plots will be revealed and the enjoyment would pick up from there. 'Accel World' deviates almost entirely from 'Zegapain' concept except for the fact that the characters are able to go to another world. Romances and battles are what makes this series very delightful to watch. Sure people who dislike the MC at first due to his looks (not a lot of series have MC like this) but just be open-minded and the series should sink into your head in no time. read more 

Stylistically, both animation and story are similar. Both center around a youth who discovers that there is much more to the world than he thinks there is, and is thrust into the midst of a battle for the world, his friends, and himself. 

Both animes have a dark tone. Both are slow shows that involve plenty of character development, some sort of memory loss, hints on big mystery. Zegapain, however, is more flashy because of its mechas, but the atmosphere of the story is similar to Persona Trinity Soul. 

In both anime the main character is introduced to a brand new world/game by the female. Both are also interesting in their own ways and I'm sure if you like one you will like the other.