Tough call, this one is really gonna depend on your preferences... I happen to live a block from Kennedy School and have worked for years just a couple blocks from Crystal, so I feel well-qualified to speak about both areas...
The fact that you'll be without a car is important because it favors the downtown location. At Crystal, you'll be within blocks of most major bus lines + all MAX/Streetcar. From Kennedy School, there are two 'main' routes, the '73' along NE 33rd and the '72' along NE Killingsworth and Alberta. While I wouldn't call either 'convoluted', you should note that neither connects directly with downtown (i.e. both require transfers on either MAX or another bus line). One nearby line that DOES go straight to downtown is the '9' Broadway (caught 7 blocks from KS front door at NE 27th) - it also goes through some very pretty & historic neighborhoods. I take all three of these lines regularly - feel free to send me a message or re-post to this thread if you want specifics on each line.
Yes, a TriMet day pass works on all forms of transit, all day - currently they run $4.75/day for All Zones; there's also a 7-day pass for $23 so, if you're in town 5 or more days, a better deal.
As for nearby amenities to your two choices, Crystal/downtown has the obvious advantage with sheer quantity of restaurants, shops, etc. The location is right on busy West Burnside, so there is some noise/traffic to expect, to go along with all those Pearl District spots, Powell's Books, etc. Kennedy School is certainly quieter, and has the advantage of an on-site movie theater, a couple extra cool bars (Boiler Room, Honors, Detention, etc) and an indoor/outdoor restaurant (the Courtyard and it's outdoor hearth is GREAT in the Fall). Most of the good places in walking distance of KS are at the Killingsworth/30th intersection (DOC, Cocette, Autentica, Yakuza & the renowned Beast - if you watch Top Chef Masters, that's Naomi Pomeroy's place). New Seasons is a good local grocery chain and Concordia Ale House is a solid taproom, both a block away. There are also a number of restaurants and bars on nearby NE Alberta St. - some upscale, some divey and everything in between.
As far as McMenamins hotels go in general, ALL rooms come *without* phones or TVs (that's part of the concept, get out and explore/socialize/spend...). Most of the rooms at Crystal are European-style (meaning shared bathrooms down the hall); you pay a premium for one of the few with a toilet/shower en-suite. At KS, all rooms have private baths AND are a bit larger (each is one-half of a former elementary school classroom).
A final bit to consider: time of year. Early October in Portland is possibly my favorite couple of weeks in the entire year. A big reason to choose Kennedy (which you alluded to already) is the neighborhood. The foliage should be gorgeous, the nights crisp and (fingers crossed!) dry...and that aforementioned outdoor fireplace should be roaring and making everything around it smell great (in my opinion :-D ).
Choice is yours, but I hope this helps.
Edited: 10 May 2011, 0:07