In looking at the motivations of many "whales" often reveals a sort of old school arts patronage mentality of wanting to support the game. If you could simply get the patron whales to pay then you could leave everyone else who won't ever pay alone and not have to force pay walls or annoyances into the actual game design. If the small minority of players that are paying the majority of money are doing so not because of designed frustration then why do it?
Kickstarter is a decent example of pay what you want patronage, but it is generally designed for starting production and free to play is based on pay as you go.
Only some players realize in app purchases are essentially funding continued development of the game. When players don't realize this they will see IAP and paywalls as greed even when its essentially a shareware or nagware model.
One possible solution I see is to use honesty in your favor, put IAP in that is directly and visibly tied to potential feature development. Vanity items would probably be best. You would retain control of the feature design, but players would vote on which features are worth the money with their actual wallet. Kickstarter reward tiers and stretch goals provide a decent model for this. Want that cool new PvP mode? Then buy this special piece of PvP gear that represents it!
There are some downsides of course. It's complicated to raise money in a way that you can refund (Kickstarter style) vs keeping the money either way (Indie Go Go style). This model can also lead to the whales directing the feature development of the game, but if the demand is high enough from small payers for a feature it can still make its funding goal. In a way this makes everyone playing the game a potential shareholder in the feature design without relinquishing creative control. You as the game developer also get to decide which features are up "for sale" so this doesn't ever have to become "design by committee".
Part of this thought was inspired by an interview with the developers of Dwarf Fortress talking about possibly working on the game for another 20 or 30 years as long as there's enough people helping support the costs for what is a free game. Sounds like patronage to me.
Why is this better than just asking for donations? Donations are all well and good, but it feels a lot more compelling when you know how your money will be spent and who doesn't like to feel a certain level of influence and power over a game you like in exchange for some visible status? See humble indie bundle (or indie royale bundle) leaderboards for an example.
One final downside is that with traditional IAP players don't know how many others have made that purchase and the amount of profit to be made from it has no inherent ceiling. Selling IAP for feature funding would need to be clear how extra money would be spent (assuming the amount raised so far is displayed). This means you'd need to factor in "hidden costs" like support, bug fixing, marketing, etc.
Hope to see some more diversity in business models for games outside of copying whoever is getting rich at the moment.