EXE4. Hit, or miss.
EXE4's pros were that the systems were rehauled and upgraded vastly, and had some more interesting bosses. Laserman was arguably the best pre-final boss we've ever had in the series as well in my opinion. The miss was that the plot structure was bad, and you more or less had to go through the EXACT same thing with the exact same length about 3 times to get a 100% run. And that's if you didn't miss anything.
Even so, this really was one of the most interesting and enjoyable areas I can recall, with one of the best scores to ever grace EXE. It definitely felt as though you were about to go up against something massive, and for those of us who didn't know Duo was the final boss, it would end up being a massive treat and a burden due to his difficulty when compared to the first 3. And you captured it completely. I really have to say that amongst the final stages, EXE4 and EXE3 were my favorites in terms of music. EXE3 in particular, since it gave a sense of "Alright, this is the last thing we have to do, so let's do it right. Nothing will stand in our way as long as we're together." like most battle anime/manga endings, and it was really touching music when you start listening carefully.