Beckdawg. . I think your over analyzing this too much..
You're welcome to your opinion. But the fact of the matter is if it was not a big deal teams would call up players whenever they wanted and they rarely do. In the cases you cite, Harper didn't sign a traditional contract out of the draft.
As reported by Adam Kilgore of the Washington Post, Harper signed with the Nationals in 2010 just minutes before the deadline for clubs to sign draft picks. He agreed to a five-year, $9.9 million contract -- a major-league contract, which is rare for draftees.
As such, Harper wouldn't even be eligible for super two regardless. Trout on the other hand wouldn't have earned super two. This is part of the issue his agent had with the team because in his third year he was set to make $510,000 and this season would have made $1,000,000 before they did the long term deal with him but still wasn't eligible for arbitration.
This year the biggest super 2 guys were Hosmer and Belt. The year prior to that the biggest player to reach super 2 was Everth Cabrera. Year prior to that biggest guys were Jay Bruce and Chase Headley. In the case of Trout and Belt, both have a very similar amount of time. Both came up in 2011. However the difference between them is Trout currently has 2 years 70 days of service time and Belt has 2 years 128 days of service time. You're talking about 58 days on the active roster. That was a difference between 63 games for Belt in 2011 and 40 for Trout.
I get why people are impatient. But you're often talking about less than 30 games. Most players will struggle to put up 1 WAR in 30 games. If you look at someone like Bruce who was a super two guy, his first arbitration year would have likely cost around $500k without super two. He signed a long term deal like you would suggest. Instead of $2,791,666, $5 mil, $7.5 mil, $10 mil, $12 mil he got from his deal he would likely have been more like $500k, $2.8 mil, $5 mil, $7.5 mil, and $10 mil. So something as little as 30 games can cost a $11.5 mil difference over 5 years.
That doesn't seem like a lot of money. It's only like $2.2 mil per year right? Well consider that Jackson got a 4 year $48 mill contract and Sanchez who was their first choice got $58.2 over the first 4 years of his deal. Perhaps that's cherry picking an example but it goes to show how little things make a big difference. If Castro hadn't achieved as much service time in his first 2 years maybe the front office has enough money to compete and grab Sanchez. Like I said, I get the concept that there is no cap on what you can spend. But, I just gave an example of a way this current cubs could have been better within the salary confines had they waited roughly 80 days in 2011 to call Castro up.