I will answer from the perspective of a software writer, and someone that was recently married.
First, as dpollitt mentions, you're not gonna get any software that will make illogical people act in an ordered and logical manor. You're at a party. People will be happy, sad, both, angry, drunk, snobbish, smelly, loud, timid, and just about everything in between. Getting a piece of software that does any kind of process requires the consent of the group. And you're not going to get even close to consent. It's likely you won't even get the group to agree on what consent means.
Now, from our side (as a customer, and people will have different opinions as customers), we told our photographer, we want such and such a shot (like walking down the aisle or getting out of the limo). Then we said we wanted structured family shots.
What our photographer did, was work with us and the venue. He made sure that as soon as the ceremony was over, before anyone even had a chance to move enough to get out of their seats, the staff brought in drinks and appetizers, and basically created a kind of blocking wall that kept everyone in the same area. Then he got the formal pictures. The entire process was done in about half an hour. For our part we instructed the bridesmaids and groomsmen to quietly tell everyone to hang on for pictures. Then we outright banned cameras of any kind. The only way you were going to get a picture is if you worked with our photographer. We also instructed the maid of honor and the best man to work with the photographer, and "pre-fetch" anyone that had wandered off.
Lastly, we instructed the "key people" (parents, and family leaders, etc.) to spread the word that this photographer needs to get through some "scripted" shots, then whatever they wanted all they had to do was ask him.
All in all, our process was smooth, our photographer was awesome, and it was a great experience.
The KEY things our photographer did to make that happen, was work with us. He suggested strongly that we move things around and have the appetizers and drinks act as a wall. He told us what needed to be done, and then let us find out how. Most importantly, when the time came, he took command of the situation. He was quite, polite, and firm. We knew he was going to do this, he told us, so we backed him up. "But I don't want to take a picture like that." was responded to by me or my wife with, "This guy is a pro, you will do what he says, that's why we hired him." That kind of team work kept the party moving and the pictures being taken, and it was a wonderful experience.
So my advice to you is:
- Play the people, setup some kind of distraction so they're not all just waiting in line like some horrible high school dance.
- Work with the bride and groom, tell them what to expect. They have a lot of power on that day. Use it to your advantage.
- Work with bridesmaids and groomsmen. Remember they're kinda the staff of the wedding. Use them as such. It's part of the deal.
- Try to find some way to make "your" pictures more valuable. My wife and I banned cameras (our photographer was shocked). That was our (really my) rule. I didn't want 100 crappy shots on Facebook. But you don't have to go to that extreme. Just make it so that people feel like "Well if I want the X shot, I need to wait my turn/work with the photographer." Maybe this can be the "only" shots of the dais. Or with the "big lights" etc. etc.