The problem with DDP2 is that it looks a lot like DDP MicroMachines edition
The perspective is too forced and seems 'straight' and 'flat' most of the time, and even where they've recycled graphics, they look smaller (maybe due to resolution differences) The explosions are ugly too, and everything just feels a bit weedy. The title screen background is horrible too.
What IGS did do a good job of was actually marketing it, localizing it, making it accessible to people outside of Japan. They have title screens for different regions, detailed how to play screens, internet rank features, practice mode... This is an area in which Cave really fail. IGS also did a good job on the protection, integrating it tightly with the gameplay and actually using it to accelerate bullet processing etc. DDP2 pushes the hardware a lot harder than DDP3 / Ketsui even if it's a far less impressive looking game.
(ignore what you see on Wikipedia, you can't change the region with a Dipswitch on the board, it's provided by the protection device, people have clearly just seen that MAME has a 'dipswitch' for it because they don't emulate the protection device yet)
I'm surprised they didn't respond to criticism and reset the score on later revisions of the game, it does seem to be the most common complaint about it, and it would be a very quick fix to make. I guess they consider it a feature tho, part of trying to make the game more accessible rather than hardcore.
You can see in part why Cave wanted to partner with IGS, but it's not really clear why they simply left IGS to make a game from their old assets. My best guess would be that Cave wanted a tech demonstration for the hardware, to prove it was a viable platform for their games, and offered a decent level of security (which they then chose to ignore)