When we purchased our home in the spring of 2011, we little room to negotiate changes as we had to remain firm in our purchase price. In fact, we 'sacrificed' the hardwood floors and ceramic tiles that were considered standard options to gain in other areas. Those things we gained were: larger vanity in the master bath with dual sinks instead of the small standard single sink vanity, a shower and oak linen closet in the small bath instead of the washer & dryer hookup that was standard, a closet installed in the room over the garage, and a pillar and ledge in the entry instead of the small full wall. On a little side note here, the pillar and ledge we negotiated into the deal (my idea), was so well liked by the builder that he put it in as a standard thing in the rest of the homes on the block that were similar to ours. :)
One of the paint colours I chose for the walls, a gray, didn't turn out the same shade as the chip (it was a Benjamin Moore colour that was mixed in another retailer's paint). I later found out they used very cheap paint and took a lot of shortcuts in application, creating a sloppy mess. So, although super excited about my 'custom' home, I was always kind of frustrated at how 'off' the colour scheme looked. Although I received lots of compliments, inside I was disappointed and frustrated at the end result.
Because of being limited to choosing only 3 colours (or paying a lot extra to choose more), this same grey is also in both girls' bedrooms. But, the main level of my two-storey house was the main source of my frustration. The gray on the walls of my living room had a definite green pallor to it, while the carpet that looked charcoal gray in the showroom actually has a brown hue in it. So, not only did the living room not look right, it was clashing with the open concept kitchen/dining room that had a charcoal gray in the flooring as the two floorings met.
Then, I found that my white appliances made my kitchen look so cheap. I had chosen darker stain cabinets (because I really love dark stain) with traditional oak trims (to match my existing oak dining set). Nothing was coming together the way that I had hoped.