First of all, read this book from Morrowind: http://www.uesp.net/wiki/Lore:Arkay_the_Enemy

So perhaps they were intending to add a guild for each temple as well but (because of time problems) had finished the temple of Arkay but not the mages guild (nor any other temple) and derfor moved the questline to the mages guild. I mean this practicly opens up the mages guild questline, but for the temple of Arkay...

I highly doubt that Bethesda ever intended to develop guilds and subsequent quests for each of the Nine Divines. One for Arkay would have been interesting as a counterbalance to the Mages Guild solution to Manimarco, but this really was more of an ancient beef between KW and his old patron, Vanus (who founded the Mages Guild).

Anyways, this really belongs in another forum.

Well,I heard churches were meant to play a bigger role in Oblivion,its possible they were going to focus more the churches' connection to the God it is in the name of,but due to time problems never happened.

In Daggerfall, I think there were factions for each Divine. They were removed in TES III and IV because those games were much smaller scale, relying on fewer guilds with unique questlines.

In the Imperial City as it really is - not as it was scaled down for practical purposes in Oblivion - there's a cult for each Divine and a hundred other gods. The Temple of the One is supposed to have gained a lot of political influence in recent years and taken a lot of focus off the smaller cults. I prefer to believe and imagine they still exist though. In Morrowind you get more of a sense of that as the Imperial Cult quest givers tend to favor one Divine or another.

I think the reason it was in Daggerfall was because all quests were random... now that there are specific quests it would requirre tons of more work... but perhaps since Skyrim uses random quests we'll get a faction for each god worshipped in Skyrim...
and btw, if it had been inplemented as I think it might have been intended then Manimarco would have kicked Arkays [CENSORED]...

I don't think all or even most quests in Skyrim are going to be random. And the ones in Daggerfall weren't truly random either. It's more like they were randomly rolled from a list containing things like cave location, item to collect/monster to kill and reward. There were many static, pre programmed quests as well.