I believe the problem is the design as a whole and not direct injection per say. Heavy diesels run direct injection and don't have the fuel dilution and valve deposit issues despite running well over a million miles before an overhaul.
In port injected applications, deposits are prevented from building up on the back of intake valves due to the constant "washing" of the valve by the injector, and gasoline is formulated to perform this function.
With a DI engine, there is no washing of the valve, so anything present in the intake air charge can leave deposits on the back of the intake valve. Over time, these deposits build-up and can cause a reduction in performance and economy. Recall the recent thread about the DI LS engine in an Escalade that never had its intake valves cleaned, but economy was clearly reduced due to build-up and eventually it had a valve get burned from deposits, holding the valve open, and needed a new head. But this was at well over 200,000 miles.
What causes the deposits will vary depending on the design, but with a closed PCV system, one of the culprits will always be crankcase effluent, the constituents of which are gaseous combustion biproducts and volatized oil fractions, but also vapours comprised of oil droplets, moisture and whatever else that can flow. Windage trays and scrapers are employed to reduce oil vapour, and limits on Noack are employed to reduce volatile oil flash-offs, but combustion byproducts will always be present and gaseous contaminants and extremely fine vapours will not settle out in separators and ultimately make their way into the air intake stream.
Another major contributor is EGR. Exhaust is dirty, so mixing it with the air intake stream will lead to deposits. when no cleaner is present to keep it washed off.
Various mitigation mechanisms have been employed over the years. Ford used valve timing to eliminate both EGR from the intake stream (rather, using reversion to bring some exhaust back into the cylinder) and to try and expose the intake valve to a bit of the air/fuel charge, in an attempt to keep it clean. This is what was employed on the Ecoboost.
Toyota famously put hybrid/dual injection on their higher end cars, the argument at the time was that it allowed for better operation, as certain conditions are better suited for port injection, but the biproduct was of course that intake valves were kept clean.
At present, it seems that many of the marques (including Ford) are just going to with this approach (hybrid injection), which, as noted above, is argued to have benefits that extend beyond just keeping the intake valves clean.
And of course DI has issues that extend beyond just IVD's. Fuel dilution has been a huge issue, and DI soot has created wear issues. Both of which impact the long term durability of the lubricants. LSPI was another unexpected side effect.
