TB, how is the truck primarily to be used? You mentioned hauling your bikes - is it routinely hauling, or just occasionally? And what about towing?
All the new trucks seem really well engineered, but here's a few things I've learned since my wife started into the truck world...
1. Will you be the only one driving? If not, and your SO is very short, you might want to look for adjustable pedals. Sounds dumb, but it allowed my wife to have a much more comfortable driving position (otherwise she'd be jammed against the steering wheel because she is too short!) I think a power seat would be nice too, but surprisingly both trucks she bought had power pedals but not seat...
2. The extra 12" of wheelbase from the crew cab-5.5' box or extended cab-6.5' box (about 133" wheelbase) versus crew cab - 6.5' box (about 145" wheelbase) might not seem like much, but it makes a BIG difference in turning radius (and ease of parking). If this isn't going to be an issue, then no worries. But if you really want the crew cab and don't want to go long WB, yet need a longer box for your bikes, would the bed extender (tailgate thingee) work?
3. You mentioned the axle ratios - if possible test drive various ratios for each engine. It makes a big difference, not only in towing capacity but in daily driving. The same engine with a 3.31. versus 3.73 might feel very different. How much of an impact the axle ratio has on fuel economy, not sure. If you are buying used, be prepared for the owner (or dealership) to not know the axle ratio - but it's easy to get from the VIN codes.
4. If you are often parking outside, tonneau covers are awesome. Even the cheap tri-fold or soft roll-up ones are worth it. But if using the bed all the time, or need more security, I'd look into the retractable roll-up hard cover ones. Very pricey, but nice.
5. If you are constantly hauling stuff into/out of the bed, look at the tailgate and bed side heights. The newer trucks are generally a PITA to load/unload (even with the tailgate steps and whatnot) because they are so high. But the various trim levels can change the height by quite a bit - 4x4s are generally higher than RWD, off-road packages are taller still.
6. If you go with a truck, the truck accessory world is ridiculous, and awesome, and sometimes ridiculously awesome! So much stuff that makes you shake your head in disbelief, or else go "how could I live without this?" And sometimes at the same time!