The last section of Evangelion suffered greatly from a combination of a mental breakdown by the director and extremely poor budgeting by the team in general. Lack of budgeting is a consistent issue that Gainax, and the subsequent Trigger, suffer from throughout history lol.
The merit of Evangelion lies in its strong story telling, cast, and action in the first sections of the series. The last part is intriguing and can leave a lot to think about, but it's hard not to look at it as just mediocre attempts to try to compensate for a lack of funding.
That being said the series as a whole serves a nice purpose of being a fantastic deconstruction of the mecha genre. In the seventies super robot shows were for the most part happy go lucky kids summoning giant robots to battle out against crazy stuff. It was fun and campy. Eighties mecha was a little more grimdark. By the nineties the genre was really starting to slow down and Evangelion came in and picked apart the conventions by presenting a protagonist not so eager to pilot a mech.
It's hard not to look back and think of the franchise fondly as it really rejuvenated the genre for a lot of people, and also is one of the heavy hitters for complex anime. I can understand how people these days may not be able to get into it though.
It's a weird comparison, but I would say Evangelion is somewhat to the mech genre as Watchmen was to superheroes. The more familiar you are with the conventions and traditions, the more you can appreciate what it was trying to do.
And of course the mechs and fight scenes are top notch so it's still awesome all the same
