I will use these two boats to illustrate three design aspects that are important to me. The Explorer is superior in all three aspects, in my opinion, but only because they are more conducive to my paddling style and favored waters. Other paddlers could reach opposite conclusions, but these design aspects are at least something to think about for a new buyer.
1. Secondary stability -- I like a canoe that has progressively increasing secondary stability all the way up to the point where the rail is buried. You need this kind of confidence in solid rail-burying secondary stability in white water -- to peel into and out of eddies, to lean upstream, and to take waves sideways when you are cutting laterally across a turbulent river. The Explorer has this kind of secondary stability, and it has been a very popular and reliable canoe, both tandem and solo, for whitewater river running and whitewater river expeditions for 30 years.
I am not an expert on Wenonahs, but most of the ones I have tried, possibly not including the Spirit II, do not have progressive-to-the-rail secondary stability. With their bubbled sides and tumblehomed gunwales, most of the ones I've paddled have a maximum secondary stability point about 3" or 4" from the rail, after which they go OOPS. This is consistent with their primary role as flat water cruising and racing canoes. I don't think I have ever seen a serious whitewater tandem team in a Wenonah canoe.
2. Seats -- I like webbed seats (preferably with contoured front rails, a la the Conk seat), which allow me to kneel or sit. I am primarily a kneeler. The Explorer has webbed seats (or maybe cane). All the composite (but not Royalex) Wenonah Spirit II's I have seen have tractor seats. Tractor seats, like tumblehomed sides, are consistent with flat water cruising and racing using a sit 'n switch paddling style. I prefer the kneeling and correction stroke paddling style, with occasional sit 'n switching, and therefore don't like most tractor or bucket seats. (The exception is the Deal kneeling bucket seat on the Hemlock SRT.)
3. Ability to Solo -- There are five reasons why the Explorer, in my opinion, is a superior solo canoe than the Spirit II when paddled stern first (i.e., without installing a center seat). First, you can't sit backwards in a bow tractor seat at all. Second, even if you could sit backwards in a Wenonah bow seat, the Spirit II has a thwart directly behind the bow seat, which I don't like in any tandem. Third, the Explorer has a more symmetrical sheer line than the Spirit II, and hence should be able to handle waves better when paddled stern first. Fourth, the Explorer is simply more maneuverable for a solo paddler because it is a foot shorter. Fifth, the more solid secondary stability of the Explorer allows a solo paddler to bury the off-side rail with more confidence than a Spirit II in order to reach the water with cross strokes and braces.
The Spirit II is likely faster than an Explorer on flat water, especially when paddled sit 'n switch. Many paddlers like tractor seats better than web or cane. Many paddlers like sit paddling more than kneel paddling. Many paddlers have no interest in burying a rail in order to turn. Many paddlers have no interest in paddling whitewater.
Therefore, the three design aspects discussed above are more or less important, or can flip in importance, depending on what kind of water you paddle and what kind of paddling style you like to employ.