Organizing my Player Collections

I have a question that I hope some people can help me answer. How should I organize my player collections? So far I have determined that:

In toploaders will be:

-Autos

-Jersey cards

-Serial #d

-RC cards of the ones likely to make the hall of fame

In semi-hard protectors will be:

-all other RC cards

-nice inserts

-higher end base cards

-SPs

-Variations and parallels

However, this is where the conflict arrises. I currently have all other cards of the players that I collect in individual penny sleeves. They are then organized by the priority in which I collect the player, and then finally by year.

This makes for a disjointed looking collection that is difficult to view. How should I change this?

I have formulated a couple ideas:

The first being: Keep the organization similar except have the cards in 9 pocket pages rather than penny sleeves.

Advantages: Cards are easier to view, I can leave blank spaces to indicate where cards that I am missing should be, and players can be separated by binder.

Disadvantages: Still reasonably disjointed, sets may end up divided across two pages in cases where the player has multiple cards in the set.

The second being: Using 9 pocket pages and binders, divide my collection predominantly by set and year rather than by player. Then organize the cards of each set by priority in which I collect the player.

For example: I would have a binder for 2009. This binder would be divided into sections for each of the 2009 sets. Then within the section for each set I would place all of the Derek Jeter cards first, the Ichiro cards after those, the Joe Mauer cards after those and so forth.

Advantages: Unified look, easy to identify which cards I need, spaces can be left for players that I am missing from each given set.

Disadvantages: The collection for each player will be scattered across multiple binders

I am leaning toward the second idea for the simple reason that this organization will serve only for the base cards of lower end sets. These are the cards that I don't care to "show off" as much and therefore it hardly matters that not all of the Jeters or Ichiros, or Mauers will remain together because the more rare and flashy ones will remain in their nicer protectors, and will be sorted by player.

What does everyone think? Questions? Comments? Suggestions? Is anyone confused?