I've read a lot of people have trouble with the final boss but I somehow don't have much trouble against him. You've got the Prevasion Chain equipped so make sure you're not attacking when he's going to hit (obviously...), use a gun with a lot of tags and concentrate them on his "core" when it's open, constantly double tap down while you're getting hit to instantly recover EP and not receive damage, and save your skills for HP recovery (except maybe the sword thing if you know you're gonna hit hard). All of that may sound really obvious, I'm sorry. In order to get the real ending you actually have to beat the last stage, boss included, with a special item equipped instead of Prevasion Chain, making this fight a lot harder. Are you having trouble with a specific attack?
I can't remember exactly what I had equipped when fighting him, but this is what I have equipped now. Skills: Astrasphere, Voltaic Chains, Luxcalibur, Galvanic Renewal. Gear: Vasuki (I like this gun since as long as you hit something it redistributes the tags among the enemies on screen, but something with more tags might be more useful against the boss), Dynamo Eye (max EP by 120), Flash Focus + (less EP expenditure), Boost Band + (double jump), Prevasion Chain. I probably enhanced some of the equipment after beating him but I don't think I changed things too much. I'm Level 60 now but must have been a lot lower when fighting the final boss since I only did most of the challenges afterwards.
Sorry, I know I'm not of much help. This is the
OT and this is an
impressions thread from when it came out. There's probably a lot better advice in there than what I just gave you. Keep at it!