I would absolutely buy a 2008 or later. I have a 2005 330 Express. I'm 6'2", and I find that the upper windshield frame is directly in my line of sight. It SUCKS! I'm constantly either slouching down to look through the windshield or stretching upward to look through the Eisenglass. I do this all day long, and at the end of a long day on the water, my neck and back ache like hell. I would kill for that taller windshield.
The bilge access on the pre-2008 boats is a major problem too. I've gotten to the point where I no longer screw and caulk the deck portion of the hatch. I have to open it all the time. You can't even check the oil on the generator without pulling up the deck hatch. Without being caulked, it leaks rain water and salt water from the washdown into the bilge, and I just pump it out. Definitely not ideal.
I also would much prefer the folding ladder on the 2008 model. I spend some time out on that boat by myself and am not 100% sure I could get back on board without that ladder. A safety concern for sure.
One more thing I wish my boat had...chiller plates. When I bought the boat in 2010, I thought that was an unnecessary extravagance and didn't put much priority in them. I fish two or three times per week in the summer with a crew of 2-4 guys. I keep the helm drink box full of beer, water and soda, and it's constantly getting hot on the off days and then chilled again with ice on the days I fish. It's a pain in the ass. I also fish for giant bluefin tuna in the Gulf of Maine. I only get a fish about every second or third trip (at best!!). I keep 150 pounds of ice in that fish box which goes to waste every time I don't catch a fish. A chiller plate would keep that ice frozen until I need it. My boat's slip has shore power, so the chillers would run constantly, and I could run them offshore with my generator if I wanted.
All that being said, I do love my 330! I use it pretty hard (over 200 hours a year) and in some rough conditions and it's held up well these last ten years. I re-engined it with F300's in 2015 and really love that boat/motor combination. In my mind, a 2008, or later, boat with F300's (and chiller plates) would be the perfect boat.