We've stayed at the Grand Pacific Palisades, the Hilton Garden Inn, and the Holiday Inn - all in Carlsbad. Here's my feedback on each:
Grand Pacific Palisades - Closest of the 3 to
Legoland (there is even a way to walk to LL if you want). Front desk was not friendly. Service is not great. It is really geared more towards people who own timeshares, or who are doing the timeshare tour. If you don't mind doing the timeshare tour, you should google grand pacific palisades timeshare or legoland timeshare promotion. There are some great savings. The grounds are really nice and it has a great pool area with a great play area for kids. Also, the on site restaurant (I think it is called Karl Lagers) is excellent.
Holiday Inn - Very simple accomodations. 2nd closest to Legoland. Probably the least expensive of the 3 and they used to (probably still do) give free meals for the kids at their on-site restaurant (which I think is a TGI Fridays).
Hilton Garden Inn - The hotel is relatively new, so yes it is clean. The rooms are small, but comfortable. The pool area was nice. It is across a busy road from the beach. I liked the hotel a lot. My husband didn't like how busy the road in front was and that another road wrapped near the hotel in the back side. It is the furthest of the 3 hotels from Legoland, but not far at all.
We personally prefer to stay in San Diego for SD activities and Carlsbad for Legoland. It has just suited our schedule better. However, if you don't want to do that, it sounds like you are doing more in SD and it might be better for you to stay there and drive up to LL.
I haven't really gotten to the point with LL where any hotel is my favorite. My son keeps wanting to return to GPP because of the pool area. I like the HGI because I get Hilton Honor Points (we stayed there for free on them last trip). The Holiday Inn was simple, room was largest and it was fine, too.
I know that a neighbor of mine stays in the village area of Carlsbad at a hotel that they really like, but I can't remember its name. I think it may be more of a condo.