IMHO:
The KLR wins in the maintenance field if you look at how long it takes to service the bike. It's easier to get where you want to get especially on the older models. The TA wins requiring less specialised tools and less stock on the shelf. You don't really need a torque wrench, no valve shims, but you might want to get a set of 2 vacuum gauges.
I'd therefore call question 1 a draw. Both bikes are not the
very easy ones to service (unlike the DR650SE) and require some level of mechanical skill & tools to do the full scheduled maintenance. Pricewise the cost of TA air filters and fourfold spark plug consumption probably cancels out the cost of KLR shims. I'd rate both bikes close to each other and near the lower end of the price scale looking at service consumables.
I don't think spares availability is an issue for any of the two. Makes 2 a draw too. You won't need to buy much for any of the two.
Offroad capability: The KLR is the clear winner
potentially. There is more of an offroader hidden inside the KLR. Unfortunately you have to fork out some 5 Gorillas (all fitted) for things like fork springs and a shock rebuild with a stiffer spring to unleash the KLR's true offroad potential. In standard form the KLR's advantage is pretty much reduced to the 21" front wheel and the larger choice of knobblier rubber.
Since you require the bikes to cope with mostly decent gravel roads I'd call this undecided too. Shifting towards more technical riding pitches the battle towards the KLR, the more emphasis you put on "decent" the more ground the TA gains.
At the end of the day I think you should look into the following points to make your decision (means there are the real differences

):
How far do you want to take the offroad part? Further = KLR wins.
How important is high (=illegal) speed for extended periods of time? (Very important = The Transalp wins, simply more power)
How important is luggage and passenger transport (Both are capable enough but I think the TA has an edge over the Kawasaki)
What's your personal preference?
And finally: Are you willing to modify the bike to make it work? A no sends you straight into the arms of the Honda salesman. See "doohickey"
