Exchanges and such getting priority handling is nothing new: MTGox was doing it in 2011 (giving hosting to eligius in exchange for priority handling); and many other miners do as well. I understand F2Pool even has a paid access API. Being able to directly prioritize transactions is one of the reasons to participate in mining.
If you google 'gmaxwell out of band fees' you'll find many examples of me pointing out this-- e.g. making sure that fee estimation code isn't confused by it.
This doesn't change anything about fee market behavior: a fee is a fee regardless of how you pay it, including if its paid with service or in-kind. They'll be less need for this sort of thing once RBF is deployed with 0.12, because there will be a uniform mechanism for everyone to revise their fees.
Prioritizing transactions is also a maintained, documented and supported feature in Bitcoin Core, and has been for years:
prioritisetransaction
Accepts the transaction into mined blocks at a higher (or lower) priority
Arguments:
1. "txid" (string, required) The transaction id.
2. priority delta (numeric, required) The priority to add or subtract.
The transaction selection algorithm considers the tx as it would have a higher priority.
(priority of a transaction is calculated: coinage * value_in_satoshis / txsize)
3. fee delta (numeric, required) The fee value (in satoshis) to add (or subtract, if negative).
The fee is not actually paid, only the algorithm for selecting transactions into a block
considers the transaction as it would have paid a higher (or lower) fee.
Result
true (boolean) Returns true
Examples:
> bitcoin-cli prioritisetransaction "txid" 0.0 10000
> curl --user myusername --data-binary '{"jsonrpc": "1.0", "id":"curltest", "method": "prioritisetransaction", "params": ["txid", 0.0, 10000] }' -H 'content-type: text/plain;' http://127.0.0.1:8332/
So effectively people are making a fuss about a miner using a feature of Bitcoin Core thats been around forever in entirely the expected way. Weird.
Where did you get that impression? I suppose that, due to routing preferences, a lot of people could use a node supplied by a company subject to KYC/AML laws. The concept is definitely not designed around centralization, though. 
