This is taking bits and pieces of a bunch of peoples ideas and putting them together and adding a little bit of my own ideas, to give one idea of a full base raid system. Sorry I'm at work and don't have the time to go back and credit everyone who gave ideas for parts of this. Sorry again for the length
First have both raid types available, with the base owners choosing if they want scheduled raids or always available.
Scheduled raids:
If you don't have an item of power you can decline any and all raids proposed, these raids would just be for PvP fun and any potential inf/enh/xp rewards that the winning side would get(assuming there would be something like this) so there should be no reason to actually have to accept a raid if you don't want to.
If you have an item of power your base must be raidable, and a time must be negotiated. The time should be no sooner than 24 and no later than 72 hours from the raid is declared unless both parties agree otherwise. An initial offer should be made by the raiding SG say sometime between 5pm and 7pm cdt on any day within the next three. At this point the defending SG could say sure 6pm tomorrow is great, or those times don't work for us and negotiations would continue. There should be a large window on either side of the time requested, say 5 or six hours. So using the example above the window from 6cdt would be from 12noon to 12midnight. If no time can be agreed upon in the 48 hour period with windows like that the defending team would lose by default. Since sometimes there can be very valid reasons to not be able to muster anyone from the SG to defend a base raid once in a while, they shouldn't forfeit the item of power the first time around. Say for the first non-defense they would lose X% inf and X% extra enh/insp. The second time X+% of both and the third time they would forfeit the item of power. I don't think the item of power should go to the attackers however for two reasons, the attacking SG could have gotten lucky and been the third time this happened, and also to prevent groups from attacking once a day when they know the other side can't defend(as well as trying to force the defending sg to be there or the will lose the item) From my experience in ladder competitions on other games, you should be able to work out something within that time frame seeing as both sides basically "signed up" for having base raids, and in theory both sides actually want the item of power. Assuming this, the attackers and defenders should choose times that are reasonable or neither side will have the item in the end.
Non scheduled raids:
The SG looking to raid goes to the raid contact, or however it will be set up. A list pops up of all the Sg's that have their base set to any time raids that also have at least 1(or two or three?) of their members online at that time. They pick from one of those and get a way point set for teleporting or a door leading to that particular base that is say 3-5minutes to get to. At the same time the the SG getting attacked gets a pop up to the tune of "base defenses have picked up signs of intruders attempting to enter" and giving the members online a chance for a port back to the base to try and organize the defense.This would allow for raids anytime, but only while members of the sg are online, so they don't get ransacked while none of the members are playing. If the members online don't show up well... I'd rething your members. The defenders being able to port back also saves them from having have people just sit around in the base to defend all the time.
Other things... Breaks, sometimes people might get sick of being attacked all the time say 7 days you can make your base unraidable in any situation every two or three months. If there is a holiday coming up and you know people wont be able to accept challenges or you want to schedule a run of the Terra Volta TF you can do it.
Level balancing, personally I like challenges. Beating up on, or getting beat up by people far outside your level range just doesn't seem like fun. Maybe if anyone is outside of +/- 3 levels from the average level between the two parties they should be brought up or down to the +/- 3 but still with all of their powers.
