I think he does exactly that - it's just that he disagrees with many of us as to who our best players are, what their strengths are, and what works in modern rugby.
I can absolutely guarantee that he's not just playing by numbers, deliberately not selecting players he considers to be better, or providing a game plan he thinks his players aren't suited to. Equally, I can guarantee that he's not making substitutions because the play-book says "57 minutes = LHP replacement" - not that you're suggesting that, but plenty of people do.
It seems that once a coach loses popularity, they lose any benefit of the doubt whatsoever, and the very worst possible interpretation of any decision will automatically be assumed to be true. For example look at the criticism he's copped for replacing Smith for Ford - an entirely non-contraversial decision that pretty much any rugby coach would have made at the same point, but it's being used as an example of how he's lost the plot, doesn't know what he's doing, and in some cases, that he's deliberately hamstinging the team because of ego.
I agree with most of this and I think it's pretty uncontroversial to say that an international rugby coach is picking his idea of the best team to win a match and making substitutions that he feels will drive the same outcome.
What I find frustrating with Jones is that he is incredibly stubborn with his views and seemingly reacts very badly to being challenged on them (see Brown, Care, Cipriani, Mitchell and high staff turnover in general). The problem with this is that many of his views are based on precedents that are either old-school or simply untrue. A recent example being when he stated that "Dan Carter always played his best rugby with Aaron Mauger at 12" as a reason to start Smith-Farrell. Carter and Mauger played together in those positions less than 10 times and only once in a year when DC won one of his World Player of the Year awards. He also said that Dan Carter only played in his first world cup in 2015 at the age of 35. He played in 3 WCs and was 33 in 2015, not 35.
Before you come at me for being anal or these examples just being Jones media bluster, imagine being a player of his and hearing similar false facts/pretences referenced as reasons for your non-selection. It must be hugely frustrating. So much so that I think the players who end up thriving under Jones and becoming his favourites tend to be those who submit somewhat mindlessly to his Eddieisms. It may be a stretch, but when I look at the 2003 team and the sheer number of eloquent, intelligent and independent leaders in that era - Johnson, Hill, Leonard, Dallaglio, Greenwood, Robinson, Lewsey - not to mention the likes of Kay, Dawson, Wilkinson who have ended up in the media, it's hard not to see the contrast vs the current team, who seem so reliant on (even submissive to) Eddie's direction.
Maybe it is due to the progression of professionalism and the impact that has, but the downward trend of your average England players on and off pitch intellect is hard to ignore and I don't think Eddie's approach is helping this in the slightest.
Also for good measure, I don't think it was a no-brainer to bring Ford on when he did, although I certainly wasn't annoyed until after the second weedy penalty touch kick and even then it's hard to argue Smith would have done much better.