Here are my votes for various aspects of each park:

Scenery:  Quetico ... more vertical dimension and more variety of tree species; WCPP is somewhat flatter and fewer large trees (if you are a food pack hanger, there will be challenges).

Portages:  Quetico for condition and ease of finding; WCPP for fewer rock gardens and distance (on average, they seem shorter to me)

Fishing:  Quetico for better variety of species by lake; WCPP has more selective species per lake...all have pike, others have walleye but no trout (and vice versa), some have all three species; small mouth action in a very few spots.  WCPP has the edge as far as size of fish and ease of catching

Bugs:  I've probably been lucky.  The past two seasons, I've made trips to WCPP in June and July.  Bugs didn't seem bad at all either time (and WCPP has no tick population).

Weather:  WCPP has more lightening strikes (most in Ontario I've been told) and because the terrain is flatter, wind can be more of problem ... both are influenced by the Manitoba plains to the west.

People & solitude:  WCPP has been a case of hot and cold for me.  On my first trip, I only saw 3 other canoeist over 12 days (beyond my own group).  Last year, I stopped counting at about 18 in 10 days.  However, as a general rule, I think you could expect to see fewer people in WCPP (annual permits tend to run under 1000 per year, where they are more like 30,000 for Quetico).

Signs of civilization:  Since WCPP is a newer park (and some of the older outposts have a grand father clause exemption), you will find more establishing/operating cabins inside the park.  And although new limits will be imposed in July, there will still be 4 lakes for fly-in traffic INSIDE the park.  (I'm assuming other lakes will continue to have fly-in traffic because of private ownership of cabins).  

Hassle factor:  It takes longer for most travelers to reach WCPP.  There is town access (Red Lake) on the east side.  No significant development on the west side.  EP's tend to be on either east or west, and I'm guessing in excess of 80% of non-flyin's use the east side.  East side has 4 significant EP's and west side is essentially 2.  The other issue of significance here is that you don't need an advanced permit to enter the park, i.e., no reservation required.  And, since this park doesn't border the US, camping fees are consistent with a north-side entry into Quetico.

Which do I prefer?  Hard question.  My single trip this year will be to WCPP.  (In the past 2 years I've made 2 trips ... one to each park.)  I love Quetico for the sheer beauty and because it offers a wider fish species selection on most lakes.  I like WCPP because it feels more like wilderness and less like park.  For example (from my limited experience) it is not uncommon to wind up on a campsite in WCPP with grass and small plants growing in the middle of the fire ring.  (I guess I should add that finding a campsite on WCPP can be a bit more of a challenge ... even some of the "park registered" campsites are either non-existent or in the wrong place ... and don't plan to drive a stake in the ground just anywhere (or at all in some places).  I guess I should add that because of historically limited staff at WCPP, they only plan to have a portage crew cover the trails on a 4-year rotation basis (with an obvious bias toward the eastern side of the park).

dd