Good article.
I agree. It gets old watching guys not run out plays at first. I understand it to a degree though, we are talking about 162 games a year, with some of them coming 10-14 days in a row. Change in weather (say from cold in Boston, to hot in Texas), possible injuries (hamstrings mostly), staying fresh for the field, etc. Lots of reasons to "jog" down the basepaths.
However, you are correct that if the players actually hustled, you never know what would happen. Yes, a runner sprinting flat out to first does in fact put more pressure on the fielders, and very well could result in a bobble or error, which would allow that runner to reach first instead of being thrown out. It's irritating that most hitters don't seem to realize that.
You know what bugs me the worst? How many times last year did you see a guy wind up with a single, yet even the announcers said he would have had a double had he been running all the way? That is very annoying to me.
As to pitchers hitting, I agree and think pitchers should be able to handle themselves in the box. I'm not saying they all should hit .300, or even .250, but they shouldn't look like little leaguers in the box either. You're right that it is fun to watch them run out their hits though. Quite a few of them give it everything they've got, and those are your true players.
Solid topic.

Yes doctor, I am sick.
Sick of those who are spineless.
Sick of those who feel self-entitled.
Sick of those who are hypocrites.
Yes doctor, an army is forming.
Yes doctor, there will be a war.
Yes doctor, there will be blood.....