Two sides of a coin to present here:
Simplest fix I can see for fixing Recall would be to change it from a skill with a long cooldown to a skill with a long debuff. Debuffs could thus be placed on all members of the guild, so swaping leader still means the new leader is 'debuffed'. Basically, think of how Guardian works. This however does not fix a few remaining issues (for example, wall bypass), but gives you something with most of the bugs fixed. The best fix I could see for this point would be to make it so that recall only works inside key locations, such as:
*The chockpoint in the middle of the figure 8 network south of the central gate.
*The coast area south of the lake, plus the cliff area in the middle of the area north of the lake.
*In the middle of both the Sheep ranch and the stonehedge.
*In any base you currently own (be it a green emp, blue emp, or the gold emp).
On the other hand, removing Recall can still present an adequate supply of alternative options. While not especially attached to any selected option, this list may inspire ideas from other players:
*Guild-wide Move Speed boost similar to Guardian, which already seems the most popular option. Each level would either increase the speed of the boost or reduce the cooldown. This skill should follow the 'guild-wide debuff' idea mentioned above after use.
*A buff which targets your own emperium, boosting some variety of survivability of that emperium by use of some kind of buff. Each level would affect this skill in the same way that the above skill would, same with the guild-wide lock debuff as mentioned above.
*A replacement of the "Kafra Token" item, giving all guild members in range an "auto revive" buff, which revives guild members where they die once. (..with the same after notes mentioned above..)
*I suspect there are those that would enjoy the skill saying that each level of skill enables you to have 1-3 allies. I'll throw that in as well, even though I'm not especially fond of it.
*On the note of making use for the blue emperiums, if each blue emperium improved the defensive potential of the guild, having a passive skill which boosts the effect of this bonus could work as well. Improving a guild's aggressive potential using these emperiums however is not at all recommended.
I'll throw in other ideas if any come up.