In addition to the Guild of the Nine, which gives you the mercenaries, the Guild of Hammers is very powerful, with its free Forges in every city. But I agree with your general point that the other guilds are pretty underpowered in comparison.
Lets be fair though. The Guild of Hammers is NOT a guild in any sense of the word. It is a wonder that results in a free building in cities in your empire, like may other wonders in BTS and Vanilla Civ. The other cities do NOT have the guild, but get the benefits. It does not spread to other cities and its presence in one city effects the entire empire. This is a WONDER effect, not a GUILD one, notwithstanding the obfuscation of nomenclature.
Beyond the Guild of the Nine, none of the other guilds seem to have any relevant or useful effect. Nothing close to on par with BTS' corporations.
Room for enhancement here.
For instance, a performers' guild that gives culture and great bard points, but consumes currency.
A scholars' guild that would give a research bonus and perhaps great sage points, but consumes food and a small amount of production.
An agricultural company that would increase food at the cost of some currency and perhaps even culture
A warrior's guild that would increase military unit production but cost food and research, and be incompatible in the same city with the scholar's guild.
A druid's council that would increase research points from forest land, but would take food, and be incompatible with arcane or priest guilds
A priest's guild that would offer units created in the city a Medic I promotion, but would drain the coffers with required gold upkeep, incompatible with scholar's guild or druid's guild
Guild headquarters (a la BTS) that would offer a greater bonus or bring gold to the headquarter city depending on how many other cities the guild is in
Exclusions which would preclude having two incompatible guilds in the same city.
Meaningful tradeoffs that would require careful consideration so that one could not randomly spam guilds, but that they could have meaningful uses under the right circumstances.
These are just rough examples in need of much refinement and revision, but you get the idea. With careful consideration and balancing, there is definitely potential for some revised guilds to increase replay value and contribute to the strategic diversity of FFH2.
These are the kinds of tradeoffs that would make builds more meaningful and bring the guild feature up to the high standards and originality of the rest of FFH2's design.
Something to consider.