Personally I loved Z4. The drastic changes in the game systems was a shocker at first but I eventually came to enjoy them. I personally loved the easier to acquire EX skills. It made the whole thing feel much more like a Megaman game should to me.
The storyline while omitting factors from the previous games did its own thing. It's much darker than the rest of the series and that's saying something for a series that's already the darkest Megaman series yet. It had heavy themes of sin, retribution, penance, forgiveness, and salvation running through the various characters.
You can see the parallel drawn between Zero and Craft, who while taking different paths both in a way are trying to do the right thing but have caused tremendous suffering through their actions, and both end up paying the ultimate price in their final act to make a better world.
Meanwhile Weil's arc comes to a close as he reveals his true intentions never being driven by greed but only an overwhelming desire for revenge, making him the total antithesis of Zero's arc. Both are responsible for a tragic and destructive history, but while Zero is trying to make things right, Weil is only striking out at the world as a whole.
Then you have Neige and Ciel. Each of them being strong support characters who drive the story. Without them it wouldn't come to this point. Both of them ultimately having to find the courage to rebel against an oppressive authority and break away from society in order to achieve their own goals. The only difference is Neige only wanted to escape, and Ciel actively fought back, though Ciel's actions clearly influenced Neige by the end who supports Zero when everything comes to its climax. You usually don't see supporting characters who are so strong as both characters and as influences on the main character in a Megaman game.
Really I'm glad for Z4. yes I'd like to have seen the mother elf and the guardians one more time but Z4 had its own narrative about redemption and death that they didn't exactly fit into. So personally I'd say Z4 is by no means a bad game. It's a vastly different game, and a brave direction in storytelling. While I can see how it can throw some people off, I love it for the strong sense of finality it carries.