Yes, Kraken goes against the grain by quoting XBT as base against LTC which is the opposite of what everyone else is doing. This is anoying as you have to invert the the price compared to other exchanges, which is nonlinear and therefore very hard to do in you head.
On the other hand, i think it's good they took the lead with this, as the market convention with fiat forex is that the highest valued pair is the base currency, with the exception of a fixed historically based hierarchy for the largest currencies, which still largely corresponds to value.
This way all rates should be above one, which makes mistakes in price less likely. Buying litecoin @ 0.25 instead of 0.025 can be a costly mistake if the spread is wide, on the other hand, whose going to type 400 instead of 40 and not notice?
Btw: in the advanced order form of kraken you can also select if you want the amount in base or quote currency, which makes it even more complex. Yet on the bottom it says something like 'estimated xxx to spend/receive' so you can alway see immediately if you're trading the right direction if you are unsure.