I don't see any real problem. There is some non-arbitrary limit being made here - namely, that they don't want domain access to be completly open for everyone to pick and choose precisely what they want. Just as it might seem a shame certain racial feats are limited to one race, or weapon feats limited to one weapon - by imposing limits on options, they are able to present more options without simply allowing players to only pick the options that are absolutely the best.
In terms of deities, the breakdown of where those limitations fall is more arbitrary, due to settings - but the same can be true of other elements. ("Why should it be a problem for my FR character to take a Dragonmark, since those are available in Eberron?) And the answer is - it may not be, and that is a perfectly reasonable area for a DM to step in and allow it as they see fit. That doesn't mean the limitations should be thrown out as a whole - just that cases where they should be are better off dealt with through DM approval more than anything else.
In terms of deities, the breakdown of where those limitations fall is more arbitrary, due to settings - but the same can be true of other elements. ("Why should it be a problem for my FR character to take a Dragonmark, since those are available in Eberron?) And the answer is - it may not be, and that is a perfectly reasonable area for a DM to step in and allow it as they see fit. That doesn't mean the limitations should be thrown out as a whole - just that cases where they should be are better off dealt with through DM approval more than anything else.