My 2¢; take it for what it's worth...
1) Ranks--I think there's near universal agreement that the ranks we have are insufficient to accurately assess members' true contribution to the guild. At least two more are needed & I'd go three (veteran, elder, sage, officer, general, champion) w/the latter being the designated leader in waiting where after a set amount of inactivity, is automatically elevated so as not to leave guilds without leadership. Program it so that an elevated champion's first act is to replace themselves so there's never not a leader in waiting. Titles are cool (War Chief, Crypt Keeper, Temple Priest(ess), Rune Master, etc.) but those could be guild specific.
2) Progress--This is tricky; for the most part, top shelf guilds on mature servers don't have a lot of guild hopping going on, but certainly it takes time to find the right fit (and guilds do morph over time--what was a good fit four months ago might not be today) whereas there's not a lot of reason to stay with lower level guilds if you aren't already "part of the family" or accepted into it rapidly. Would the progress rewards stay with a member who leaves one guild for another? (Example: @Marshall_Gawain_II leaves her guild after they earned progress marker X and joins a new guild that also has earned progress marker X--does she get to partake immediately? What about @Wilde_R_Beast who left his guild that didnt have progress marker X? Does he have to wait to partake until he meets the requirements separately?)
3) Loyalty--By far the single most useful tool that could be granted here would be the guild bank discussed in the very first reply. Yet another currency would mean nothing if the shop pricing issues discussed in voluminous detail in too many other posts to count aren't fixed. Beyond that, guild loyalty translating into battlefield improvements seems like the wrong play--this rewards simply staying put whereas the idea should be to reward continued team effort. I'd much rather see guild challenges (clear the crypt w/each member having at least 2 skulls), guild contests (largest amount of total power added in a 72 hour period) or guild records (longest streak of temple wins w/o a loss, but every member has to have at least 2 temples for the streak to count). A certain number of completed challenges could then unlock particular benefits; thus you have a proxy for "loyalty" (number of badges earned) that actually comes about by way of doing something that helps the guild.
4) Upgrades--If I understand this correctly, this is customization of toon stats based on what guild you belong to. I can see this going bad quickly; if the "research" leads to RNGesus determining which guilds gain what buffs, the elites are going to be pissed. If it's "sacrifice X amount of (whatever) to gain +Y% on all (thing)" then the rich are just going to get richer. Only way I see this working at guild level is putting in a certain percentage from each player in the guild so the sacrifice is proportional no matter where you are in the game--and even then, runes have kind of established that hero customization is done on an individual level. If the Devs are seriously considering a "forge" so to speak to upgrade weapons/armor, that really should be available to everyone.
5) Improvements--I don't think there's a lot that needs added here. Chat is unreliable, numbers of friends allowed is limiting, old convos don't drop off your PM list, you can't msg players in other guilds w/o being friends first. That you can't see your position in war/player age/number of temple kills seems like a pretty glaring omission.
Anyhow, that's how I see it. Guilds are supposed to be family; comrades in arms. For them to be that, they need to be able to do more together. War is presently the only area of the game where collaboration is paramount to mission accomplishment (the crypt and temples perhaps in small doses). If you want to give a better guild experience, then start giving us more things to experience in game as a guild.
Hope this is helpful @DSSven