As someone who has a 17.5' Lund Pro-V and an 18' Jetcraft (prop), I have some very strong opinions on the subject. I started this thread before I bought the Jetcraft:
http://www.ifish.net/board/showthread.php?t=315957
My Lund is in Minnesota, my Jetcraft is moored in the Columbia. I had my Lund out here five months last year, moored as well. I fish at least a month of fishing days a year in the Lund and more than that in the Jetcraft. Now that I have had the Jetcraft a while, my opinions are more fully-formed than they were before I bought it. Here are a collection of semi-random thoughts on the subject:
Stern height isn't so much an issue as having a full-height splash well (as high as the gunwale) or not. Many NW boats (a few Hewes models come to mind, as well as many others) don't have full-height splash wells, either. I don't see the Lund as being any less safe than any of those boats in this regard. In fact, the side height on my Lund is quite a bit higher than my Jetcraft, and I feel like I could take a wave across the side better in my Lund.
Lund isn't my first choice for a Midwest-style boat. As an earlier post suggested, Crestliner takes that title. Alumacraft would be my second, then Lund. This is mostly because I like a large rear casting deck and Lund has the smallest. The other versions of Midwest-style boats you see more of out here (Smokercraft, Fisher, Starcraft, etc.) don't hold a candle to the previous three.
If you're going to be going up skinny rivers, obviously you want a NW-style boat. If you're always fishing inland on slower water that you know well, I don't think you're gaining any advantage with a NW boat.
I LOVE fishing out of my Lund. I LOVE trolling with my Lund. This may mostly be a function of the deep V, as far as trolling. My Lund is 18-degree V. The Jetcraft is a 12-degree V. It is so much easier to hold a line with the Lund. The Lund is also quite a bit heavier. There's much more wood and storage and amenities with most Midwest boats. Mine had two live wells and a bait well. I took a livewell and the baitwell out for more room and storage.
While I'm not done turning my Jetcraft into a Midwest/NW hybrid (bow-mount Minnkota comes next), I know I won't like fishing from it as much as the Lund even after I'm done. I love having a big front deck. It's a tiller, so the "dance floor" is the whole boat. When I got a Sturgeon bite, I would actually run to the bow on the hookset to keep pressure on. If you fish walleye, you can have three or four people jigging at once. With NW boats, the bow is for the anchor, ball and rope. With MW, it's a place another person can fish. Obviously it depends on what kind of fishing you want to do. A salmon fisherman has little use for a big deck on the bow, except as a place someone with a long rod can go while you try to net their fish.
Even with the windshield being placed farther back in the boat to allow for the front casting deck, Midwest boats are usually 6-18" wider than same-length NW boats. This makes a big difference.
The Jetcraft gets on plane much easier. In fact, there doesn't seem to be an obvious point between being on plane and not. The Lund is very obvious when you're not on plane.
I've never had a problem with rivets and don't know anyone from Minnesota who has, either. That said, like the other poster, I prefer Crestliner, which has no rivets (but not because I don't like rivets). I know more people with broken welds than I do with popped rivets.
Most Midwest boats are carpeted. I love it when it's dry but not so much when it's wet. Cleaning it sucks. You wouldn't moor or store it without a cover out here.
If I knew I would only be fishing lakes, it wouldn't be a contest, Midwest boat all the way. Even now, I haven't fished anywhere my Lund couldn't have fished better than my Jetcraft. That's all that matters, really. If you're going to go into skinny water that requires a jet drive, you want a NW boat. If you're going to go offshore, you want a big NW boat with an offshore bracket or an Arima. If you mostly fish sturgeon or salmon you can go either way. If you also fish trout, walleye, bass, kokanee, muskie, pike, etc. you'll have more fun in a Lund/Crestliner/Alumacraft.
Your struggle is one of self-doubt. I had it, too. Still struggle with it. The fact remains, I love fishing out of my Lund more than any other boat I've seen in these parts. I hope I can get close with my Jetcraft. At least people won't give me funny looks, right? That's a silly reason to ditch fishing out of what makes you happy.
Good luck!