anti-painkilla :
Would you settle for a CPU because you wanted a certain motherboard? What about settle for a motherboard because you wanted a certain CPU.
With integration you no longer have the option to pick and choose pieces as you wish.
First, stop and think about how many actual motherboard variations are actually worth jack to most people who would buy a device based on an embedded CPU. Does the choice of motherboard actually matter when nearly every feature most people are likely to care about is built directly into the CPU?
Second, most devices integrating BGA CPUs are likely to be all-in-ones, tablets, ultrabooks or proprietary SFFs that have little to no internal expansion options and non-standard HSF, so most build options are already taken out of DIY builders' hands anyway... only motherboard choices are what the SFF/AiO/tablet manufacturer makes available.
Third, how many people actually need any of the tiny incremental features from the 100s of motherboard variants out there? IIRC, Haswell with GT3 graphics has on-package chipset, so distinguishing motherboards based on chipset is non-applicable and that already kills off 80% of potential motherboard variants. The BGA CPUs are clock-locked, so all overclocking-oriented features are also irrelevant, which kills off another ~70% of potential motherboard models that try to distinguish themselves based on beefed up power delivery. Since BGA CPUs are most likely to get into entry-level systems which are clearly not intended for enthusiasts, any fancy IO options are almost guaranteed to go to waste, so this kills off nearly all other potential motherboard variants. We are down to pretty much one CPU model = one motherboard model.
So at the end of the day, there may not be any variants of BGA-based boards beyond picking the CPU and motherboard size if/where applicable. Also, nothing forces motherboard manufacturers to offer all three i5-4xxxR variants on all form factors either... or offer any of them in any (standard) form factor at all.
Personally, the only add-in-board I have put in either of my last two PCs is the GPU and after GT3, I might not even need that in my next PC. The motherboard choice is of very little importance to me as long as it is both reliable and affordable, so BGA CPUs are perfectly fine with me if it makes them ~$25 cheaper (cost of socket and part of the cost of the discrete chipset on LGA motherboards) than their socketed counterparts.
Intel's upcoming BGA-based Haswell solutions may not be ideal for everyone but what Intel packs in them will certainly be enough to address most people's everyday needs in more convenient form factors.