I like the idea, you have really convinced me to use "party", the only problem I have is that I have to adapt it to the gamplay I already have planned and especially to the story, by expanding the guild a lot certain characters could lose the prominence they already have.
That is were the "lone wolf" idea can come in handy. If you get what I mean. Especially if you can only do so much with the mechanics that the engine lets you use. But do what you want to do. It always depends on the max amount of characters you want to use for the harem. A party system could develop a "party personality" amongst the characters in it. AKA romance the "(special named)" party. If that is a possible idea. If it makes it easier you could use the name (icon) of a certain party to do certain jobs the same way you have certain girls do certain jobs. Do what you gotta do at your own pace. Keep learning from your experience. Once you complete what you want done in this game. You could use that experience for the next game when you start from the beginning of it. Don't drop this one though. Please. You could also put some of these ideas on the back burner for the future once you get the story going really good. You could also use these ideas in a "minor way" as long as they don't over stress you. If it helps maybe you could make a name for different "parties" and then develop the love story line for those members as they come along. The main harem members will always be front and center. A big harem always has side harem characters that benefit the harem in their own way. Prioritize it like that. Especially for your first game. If you give each member equal attention then the story might not progress at the speed you may want. Once you get the hang of things "then" you could "spread the love."