DTH, I'm assuming you are considering a 2001 because of the price. As you probably know by now, each pre-owned unit has it's own unique history, which IMO is a bigger determinate of your purchase, unless you are dead-set on certain features. I believe the exterior window flaps were discontinued beginning with 2005. Although rolling them up/down on the outside can be a pita, I enjoy the flexibility to create awnings with the flaps with the proper self-made supports.
Somewhere around 2011 (?) a one-piece roof came into production. Others can clarify the year for you. There is active discussion whether people have had oil-canning issues with the new roof, but overall I consider it a good feature however you may have to pay up to get into those model years.
Since you've been a member for 4 years you probably have seen various discussions on different features, so I see no reason to go into details on the many items that longhorn and subsequent posts have mentioned. But I can give you my two cents about my experience after I expand on my opening statement: each pre-owned unit has it's own unique history which includes how the unit was maintained, stored, modified, upgraded, climate where kept, etc, which I think should be a greater consideration in your purchase.
When I purchased mine I had decided I wanted an Eagle which were no longer being made and which limited my available pool of potential acquisitions. And I didn't want to upgrade my truck until I figured out if I really liked this new type of camping (I mostly backpacked). So my first and only purchase so far is my 2001 Eagle. From looking at other models/units of the same vintage, there seems to be little or no changes from the late 90's until about 2005 (window flaps gone). This coincides with the owner who bought the company (Tom) around 2001 and probably kept things as-is for several years until he was comfortable with making production changes (now there's new owner's since Nov 2017).
I paid $4,500 for the Eagle several years ago and paid an equivalent amount in factory-performed upgrades, plus some of my own. I have at least $10k into my unit. In retrospect would I have been better off with spending the $10k on a more recent model? Possibly, but I have had fun figuring out how to customize it to fit my needs, and it's still a work-in-progress whenever I'm not using it. If I ever sell it to upgrade to a newer model, I will have a wealth of knowledge to guide my next purchase decision that could have only been obtained by prior ownership.
In my case I was the third owner, and while the prior owners seem to take care of things, there were a couple of modifications that were a little shoddy. I ended up paying the factory to install a new one-piece roof, lift boards, exterior lifters, and roof fan. The old roof leaked and probably could have been saved with resealing, but it was disheartening to chase down one leak and then find another and another (water travels in some strange paths). I did not change the pop-up fabric when the roof was being replaced as it is still in good condition (and would have cost another $2k). All systems work, with 3-way frig and furnace and plumbing. Although I'm mechanically inclined and do all my own work, I wanted to factory to do it right instead of me trying to learn on the job (and I live within an hour of the factory).
Many model changes can easily be done on an older unit by the owner. LED lighting, undercoating, etc. A friend who posts on wtw also has replaced the exterior siding on portions of two units. In some cases I think these things can be better executed by the owner as it gives you the chance to upgrade materials, insulation, flooring, etc, which is why many people buy a shell model and start from there. I have upgraded the turnbuckle anchor points on my camper too. It was a relatively easy and low-cost upgrade with factory parts and self-installation. I'm in the process of adding light-weight flexible solar panels and maybe, possibly, I might upgrade to a new frig, but the 3-way seems to meet my needs when running on propane.
The only thing I don't like about my 2001 model is the way all the weight is placed on one side. The galley, frig, LP tank, water tank and furnace are all on the driver's side, with the other side being a couch. I think this is a common layout until later years. This is somewhat a concern on my prior-century small Tacoma, which I have offset to a major degree with air bags (higher inflation on that side). Still, I would rather have a more balanced unit. Until I'm ready to do some significant changes (or buy a newer unit), I'll live with it and drive cautiously around corners.
This has been a rather long-winded missive. Hope it helps. Short answer is consider the condition of the roof and pop-up fabric, and lift panels (since they are a pita to replace unless you remove the roof). And of course stress cracks and other items mentioned in the buying guides. Anything else can be upgraded/changed as needed, depending upon your ability. You have to do the cost/benefit analysis yourself each time you consider a unit for purchase. But don't discount the value of the experience of owning one. After you know what you like or dislike the rest falls into place.
