Windsor Travelodge is very central, right by the station that serves Slough & Paddington, next door to Waitrose for picnic stuff, and plenty of chain restaurants. Shuttle bus stop to Legoland is nearby (might be free, not sure).
You might want to look at Legoland Holidays too, as they usually do good deals with 2-day tickets.
We've had family stay at the Travelodge in Windsor when they come down to visit and they've always been happy with it, but last time DHs mum came down she stayed at The Trooper, its a pub but it has separate accommodation at the back. MIL stayed in their family room which has a double bed and 2 singles. The food is really good aswell, we often eat there.
When we travel into London we usually get the Greenline coach it takes about 40minutes but it can work out cheaper than the train, it goes to Legoland aswell if you get the one coming from London rather than going to London.