You do realize that that's essentially what the two legs are, right? It is a 2-team group where you play every team (in this case, just 1 other team) home and away.
We already have the points system, if you think about it. If you win both games, then you have 6 points and your opponent has 0. If you win one, and tie the other, you have 4 points; your opponent has 1 point. If you both win a game, or both matches are draws, then you are equal on points. In a group stage what's the first tie breakers you ask?
1. Goal differential in all matches (or in just the matches against the opponent you are tied with if you go with the UEFA tie breakers, in this case being just the one team so doesn't mater).
2. Total goals scored (same as above in terms of all matches or just your opponent)
3. Total goals scored away from home (ditto)
If still tied after the above, that's where you get the funny rules of fair play, drawing of lots, etc. Since this is a 2-team group, however, you can skip those and use Extra Time and then Penalties. So in other words that's where the aggregate system comes from.
People get really fixated on the total goals/aggregate/away goals rule because it's included in the score keeping, but it truly doesn't take effect until the two matches are over. They are just tie breakers in the event you both win a game or you tie both. The only difference between what currently exists and what you are proposing is the tie breakers that prevent Extra Time and Penalties. The whole point of using goals as a tie breaker is to encourage goal scoring from both teams, and the reason for the away goal rule is to prevent teams from bunkering down when playing away. Seattle won the MLS Cup because it was a single match. They had no real incentive to attack and therefore took the match to penalties.
The aggregate rules are designed to prevent more games from going to penalties. And you want to implement changes to increase the number of series that end with penalties?