@OP... You make a few points here. Some can be remedied with minor user adjustments. Others require a change in your overall habits.
Typically, this happens when you're running an ISO or HB Dive with no double-team up front and you're hitting the sprint button while you're in the backfield. Try to stay off the sprint button until you get to the line of scrimmage...
Even so, you will still see the O-line miss blocks. If it becomes too bad to handle, run from a formation with a fullback to give yourself one extra protector. Stay on his butt until he engages - then cut away from the defender's exposed shoulder.
Common misconception... 2-3 seconds is an eternity in a football game. If you're standing there that long, you're probably also staring down a specific receiver and missing open men that break open before that...
I recommend you reset your internal clock so you measure in steps - not seconds. If your QB has time to take a 3-step drop from under center, you can run a Hall-of-Fame worthy offense (See West Coast).
To reset your clock, go into practice mode with OFFENSE ONLY. Call a pass play with a receiver running a hook route. When you snap the ball, don't throw it. Just COUNT. Look at your QB's feet and count his steps - preferably out loud. Make it a point to know how deep you are on your 3rd, 5th, and 7th steps (5, 7, and 9 yards respectively). As you plant your back foot on your drop, you should have your receiver picked out and be ready to throw so that your next step is toward your intended receiver... Timing is EVERYTHING.
Once your timing is right, you can sync up your routes and you'll have a good idea of when to be ready to run, scramble, or eat the ball.
If you're having trouble running the ball, you may not be reading the defensive front. Don't be quick to slide protect. Instead, do a count and run toward the side with the fewest defenders. Be sure to test the secondary and audible from runs/passes as the front dictates.
This happens when you press SPRINT. When you sprint, the defenders sprint. Any defender that is engaged doesn't SPRINT, they PUSH to disengage. When you see the defensive linemen break blocks at the same time, it's 99.9% because you have pressed SPRINT while still in the backfield.
Don't sprint til you get to daylight - but be warned - this is one of the toughest habits to break.
As you become more in-tune with Madden, you will begin to notice and anticipate which blockers are in jeopardy of missing their assignment before the snap.
Think of it this way - you're the offensive line coach - so you should know how your line will block a variety of fronts. Otherwise, you won't know if/when/how to adjust your blocking to account for what they might miss. Once you learn how they block (or don't) you'll know whether you need a FB, extra TE, or simply get into shotgun to buy the time you need.
Hope this helps,
Later