Qwick note(s)-
How can it be said that all of these improvements have no affect on value (as demonstrated by comps), when no house with these improvements has sold before?
You have kind of answered your own question here with your question. The effects are measured by the reaction in the market. Taking the perfect scenario.....two houses are exactly the same with one exception. One has a three car garage and one has a two car garage. A buyer may OR MAY NOT pay a premium for that extra garage. Logic would tell you "yep, a minimum of "x" amount paid for the extra garage." The buyer begins to set the bar for that third garage "upgrade." Note: one buyer does not typically set the bar, the trend does.
What if the majority of houses in that neighborhood have one to two car garages and buyers are paying extra for a two car garage but when you drive through that neighborhood you don't see a single three car garage anywhere else? Tons of variables here but if the "neighborhood" is a "one to two car garage neighborhood" then that extra garage may not contribute a whole heck of a lot to that property (or nothing at all)....buyers are not paying for it. It may have cost thousands to add on (upgrade = no added value). Now if the floor plan began with a one car garage and another were added to total two you may likely see some added value if that is what the buyers in that neighborhood are paying for. This is where a local appraiser is priceless; they will or can determine if no data = no value or if there is data to reveal otherwise (historic, current or similar markets). It always depends on that specific area and what knowledge that person has in that area. Otherwise, the buyer has to pony up the difference (a concept totally lost in typical buyer/seller market). Buyers often think that upgrading is built in to value (mostly new construction buyers). That's another thread for another day.
Right now (in many markets, not all) there are many reasons why people are paying what they're paying and so many of those reasons you just can't physically touch (emotional, financial, motivation, whatever). Whereas before (around the time when you had purchased your house) these "things" were around but in a different context and could more easily be measured. This is where the knowledge and experience part comes in. While the less obvious can still be measured to some degree, verification of this activity needs to be done on a case by case basis (and it is widely not being done by the appraiser). By verification I mean the appraiser really needs to be in touch with his/her market by speaking to the other real estate professionals in an area. This is a concept widely overlooked by appraisers and it's unfortunate (fast and quick is the status quo for many lenders and it's showing).
Questions for you and your sale are what is being offered in your neighborhood? Are you willing to wait for a buyer to pay the premium? Are buyers looking at both the other houses and yours but not willing to pay any more for yours? What's the level of competition in your market area? It sounds like yours is near closing/closed but still a few points to take into consideration moving forward (among MANY others). Your agent should
have prepared you for this scenario or at least have been able to explain it to you if it is a reality. You're in a tough spot because the appraisal reveals that buyers are not paying for them
but you have one that wants to? Either way, it does happen. You and your buyer may (or may not) have been the victim of a McAppraisal, too late to determine that. Do yourself a favor and research AMC's (appraisal management companies) BEFORE you purchase your next home. Find out how the system has been manipulated to work against you for profit and not FOR you (and the general public's) best interest in mind. Share your findings with your friends and neighbors (we would appreciate it as well). When you find a lender ASK THEM WHO THEY
NEED TO ORDER THEIR APPRAISALS FROM and research that company.
The reality may have been that the appraiser did his/her job for the lender by not valuing something that has little/no value in the current environment; it may have been over valued in it's listing/offering.
Back to you.....your question has pretty much been answered (by the posts) and I think in many markets (not all) one post says it very clearly for the majority of markets today....the upgrading is just "the icing on the cake." This is what is mostly selling properties in the area's that I cover. Higher cost/upgrading = higher return......no and not with most investments. House values don't "stand still or just go up," evident by yester-daze frenzy and today's drought. Think on a "need, want, really like it" basis when upgrading. The less somebody else needs/wants something the less they will be paying for it (even if you like it a whole lot

!) I have have formica counter tops, my neighbors have granite. I could really care less what is put on them or how they're treated (for the most part), they panic with theirs. Their house is hardly worth any more than mine for it (I like granite too though) but may sell quicker than mine. It's a very sensitive thing. Some may like the landscaping in my yard (which is awesome and my own doing) but some may go for the granite. Overdoing it is possible with any type of upgrade. Be careful!!!
Moving forward- survey your agent (or agents) in the market that you are buying in. The contribution of any upgrade can be less than, equal to or in excess of it's cost. Markets are very specific in what they will tolerate. Be sure of the value you are seeking. Whether it's for your own enjoyment or future return on the investment. Nobody can see the future (not even us appraisers) but we can see where they are and
may be headed based on the markets behavior. Staying in the "norm" is safe and doesn't typically pay big. Moving outside of the norm can bring big returns OR big loses. As a single homeowner, just treat your house like a house and don't bet the farm
Trying to outpace cost with value is tricky without some very specific local knowledge these or most days. Keep this next thing in mind too with the next house you buy....hire your own appraiser for the $400 or so. It's a lot of money to cut a check for but think of the value.
It's a drop in the bucket compared to the effort it will take to pay that loan back (with interest for 30 or so years (or potentially be upside down in right out of the gate if you're not careful!) There is a ton of value in a local appraiser, just do your homework when shopping for one. Here is a starting point for you to begin hunting if interested:
http://appraisersforum.com/showthread.php?t=152157
Good luck