"On the day" timings help needed...

Can you email the hotels eplain the situation and see if they will let guests check in early?

This - or even if they can't check in, often hotels will let you leave bags there and check in later on.

If this doesn't work out, then I think you just have to factor it into your timings for the day and make sure people know what time stuff is going to happen. If people know dinner is at e.g. 4.30 then they will be back by then - there can't be that much to do at a travelodge that is more exciting! Photos is a little trickier, but you could either put a note in your order of service or get your minister to announce at the end that you'd like people to be at the venue for x time so that nobody misses out on photos.

Every time I've been booked into a hotel I've just checked in at midnight when we got back to the hotel after the wedding.

I was at a wedding the other week that had a very similar situation to yours. There were about 4 cars between our group of friends - we all drove to the church then drove straight to the hotel afterwards where we transferred all the bags into two cars and drove the two bagless cars to the reception venue (so we could leave them overnight). Took literally a few minutes. Then we just checked in when we got back to the hotel at midnight.

I rang the hotel where most of our guests were staying and just gave them the heads up that the majority of guests would be checking in at midnight - they were fine with that. I suggested that in the invitation information for guests too.

Perhaps you could split the difference - take some of the key group photos outside the church immediately after the ceremony (a big advantage is that you've got everyone in one place at that point, and people are generally prepared for group photos happening at that point), give them a chance to check in on the way and then head to the reception, and then take any other group photos you wanted and the big group photo after that before heading in for the wedding breakfast, as you should be able to expect that people are there by then. It also means you'll have a nice relaxed time in between to chat to guests who are around and as they arrive, or you could use that time to go off and get some shots just of the two of you.

Best bet though is to have a chat with your tog and see what they suggest - they'll probably have some good thoughts of their own.

Why don't you go and do your couple shots straight after the ceremony and tell ppl to book in on their way then start reception drinks 30-45 mins later to allow for this?