Where to begin?  Perhaps listing the facets of the NFL you dislike would have been easier.
Overtime: Changes long overdue.
 Despite the fact I disagree with the majority of your complaints, in regards to the NFL overtime procedures, I concur.  The inadequacies of overtime stem from the lack of a guarantee both teams will have an offensive possession.  Overtime and its' rules should parallel regulation play as closely as possible.  During regulation play both teams kick off and as a result are granted an opportunity to play offense.  Statistically the majority of overtime games end with both teams having at least one offensive possession, however the fact your offense may not see the field is a real and distinct possibility.  At the very least allow both teams a singular offensive possession before implementing sudden death.  
My distaste for the current overtime procedures is palpable, but NCCA overtime rules are far from ideal as well.  By shortening the field, the rule effectively diminishes the role of special teams.  Kick offs and kick coverage are non-entities under these regulations.  The college system is an improvement over the NFLs' current policy, but has room for improvement. By taking the best of both current systems, the antiquated and inherently unfair NFL overtime methodology could finally be put out of our misery. The solution to the shortcomings of the present system is obvious.  Overtime would follow regulation play rules.  Each team would have an offensive possession either through kickoff, punt or turnover. If one team scores, the opponent would have the opportunity to score in response. If the team fails to score, the game would end.  In the event both teams score, sudden death would apply to the remainder of the overtime session.
This system keeps play true to regulation rules while not granting either team a discernible advantage if they possess a high powered offense, defense or special teams unit.  
THE KNEEL DOWN

How to explain the necessity of the kneel down?  Clock management and the desire to keep your players from unnecessary injury.  Last time I checked football is played with a time limit.  If taking a knee milks valuable seconds, denies the opposition an opportunity to score, prevents meaningless risks to players and helps facilitate a win, it's simply good strategy.  

THE FAIR CATCH

To say I have returned my "fair" share of punts would just be a blatant lie and I will assume your case is similar.  Eliminating the fair catch would result in several possible scenarios. Kick returns would be a thing of the past.  Unless the return man had a 10-15 yard buffer from the nearest coverage man approaching fast and with a singular goal to separate the him from consciousness, the returnee would step aside and let the kick take its' natural course down field.  Kick returnees are a special breed and denying them the option of catching the ball without high-speed blunt force trauma is preposterous.  Teams would go through a new return man every game that is if they could find anyone insane enough to accept this less than desirable task.  Kick returns are possibly the most exciting plays of a game and subjecting talented returnees to unhindered, full speed collisions would ensure one thing, an average career of about half a game.  

THE BCS

The Bowl Championship Series exists for a solitary reason, money.  Find a way around denying schools, conferences and bowl committees the cash cows that are bowl games and I'm all ears.

Arena Football
Don't care for it?  The answer is elementary.... don't watch.

CRAZY FOOTBALL FIELDS
No endorsement here for blue turf or numbering every other yard marker.
The most disturbing aspect of the Boise State Blue.......every year dozens of birds mistake the field for a body of water and become significantly flatter and dead upon landing.

MADDEN and the GOOSE
Madden's inane commentary is his bread and butter.  His popularity isn't based on deep analytical insight.  Awesome videogame designer?.....Madden's contribution to the game that bears his name is just that, his name.  

Tony Siragusa may come off as just another ex-jock fat guy, but his field level analysis is unprecedented and most likely goes over your head or through it.

GAME AVAILABILITY

Make your way to any self-respecting sports bar and check out 14 games on the NFL SUNDAY TICKET and on their dime.