I think the reason miners are not taking advantage of ways to increase transaction fees is that the transaction fees are miniscule compared to the block subsidies at the moment.
I think the average number of transactions that a 1 megabyte block can hold is somewhere around 4,200. If all those transactions included the current recommended minimum fee of 0.0005 BTC, that would be 2.1 BTC. That is an 8.4% premium on top of the subsidy. At the current exchange rate (approximately $140), that's an extra $294. Seems silly to leave $294 sitting out there unclaimed everytime you solve a block. What's the benefit to a miner of not putting the extra $294 in their pocket?
The thing that bothers me in the longer term is that miners have absolutely no incentive to include a zero-fee transaction in the block, whether it's so-called "high priority" or not.
Well there is the collective benefit of increasing the popularity of bitcoin so it attracts more users, some of which whom may pay fees in the future. (Like a loss leader in retail).
Even in the short term, because the subsidy outweighs the transaction fees by a significant margin, you might as well just never include any transactions in your blocks.
To what benefit?
Not healthy for the network! I noticed a block the other day which was the first one for about half an hour, and it only included six transactions. That is not useful miner behaviour.
Sure it is. It prevents attacks that would modify a confirmed block. Every new block contributes to that protection regardless of whether the new block has many new transactions in it.