Harlequin, I'm sorry if I misperceived your statements; so let's carry on with the time system discussion.

If we ask in what part of the game (fuseki, chuban, yose) a player can spend the largest block of thinking time on his next move, Fischer time emphasizes the later game stages more than the opening (by the way I believe that this is why wms dislikes Fischer time, based on reading the KGS wish list), basically because it doesn't "spill":
For example if you start with 20 minutes base time and get +20s on each move, that means if you play very fast during the opening, you might have about 40 minutes to spend somewhere around the middle game fighting. If however you are a player whose strengths are in the opening, you'll only be able to spend about those 20 minutes.
As you mentioned, a time system's usability depends on the actual settings. In this case, the game could probably be made fairer by setting the fischer bonus to the actual period of time a "fast" move takes, for example 4 seconds, and optionally also increase the base time to keep the total game duration somewhat similar to the example above, say, 45 minutes. Now a player could use 45 minutes right in the fuseki if he's a "fuseki person" and play quickly afterwards, or he could play quickly in the fuseki, about keeping his 45 minutes, to spend them later on when fighting arises if he excels at it.
The dilemma is that the smaller the bonus, the fairer the players are treated in terms of when exactly they would like to invest most of their time, while on the other hand a smaller bonus will move the time system closer towards the problem faced in absolute time where unreasonable moves can be played to attempt and make the opponent lose on time (or make a really big mistake).
A spilling time system has the flaw already pointed out of asking a player to continue thinking even if he already solved the 'local problem at hand', just to make sure he won't "waste" or "lose" time. On the other hand, in this system the base time pool could grant the same continuous block of time to be available in any phase of the game, not favouring either opening or later stages.
It becomes a fair guess that there just isn't THE perfect time system really.
I'd like to make two suggestions:
a) a mix of Bronstein and Fischer time, let me call it "Bronstein Carry" maybe.
Carry, because a percentage (for example 50%) of the usually spilled time will be added to your time pool, ie carries over. (So a 100% setting would result in this actually being same as Fischer time.)
The reason why I think this isn't just an arbitrary compromise but could actually improve the overall situation is as follows:
In my opinion, after the player finished thinking about the main local issue at hand, and in order to avoid spilling any time starts thinking about secondary issues, the quality of this thinking time is inferior because he cannot completely focus on it (he has to keep his primary conclusion in mind and mustn't forget it). Further, time spent _after_ your move (or after you have already decided on your move and just not yet placed it, as in this scenario of avoiding to spill time) but _before_ your opponent's move is less "valuable" than the time available to you _after_ the opponent has also made his move. Why? Because you have to consider less variations when trying to read out a sequence, since your opponent's play has probably just reduced the amount of branches to consider.
From these thoughts I deduce that gaining 50% or even just 30% of your spilled time added to your base time might actually be a pretty decent compensation that could strongly reduce the annoyance that you might feel in a spilling system.
At the same time, the bonus added on each move can be kept significantly below a comparable Fischer bonus, thereby reducing the time system's bias towards later stages of the game (if we look at the 'biggest continous usable time block' issue stated further above).
b) A "Fischer Byo-Yomi" time system.
Basically you'd have a main time same as with any other byo-yomi such as japanese and canadian, and after that you'd have a Fischer-style extended time.
Example: 45 minutes base time, 3 minutes Fischer byoyomi at +10 sec each move.
This way, you could emphasize fuseki a bit more, or rather prevent de-emphasizing it, by avoiding piling up more time later than you started with (without having to do artificial limitations that are sometimes suggested such as capping the total time you may get from Fischer bonus).
On a side note, I found a somewhat related quote in article
http://senseis.xmp.net/?TimingSystemsRedux which might be nice to know:
"An interesting report on the use of Fischer timing in New York from the American Go Association EJournal from 2006-11-06 (quoted with permission):
LIU & LOCKHART RULE IN NYC IWAMOTO TOURNEY: Xiliang Liu 7d and Will Lockhart 2d took top honors on Sunday at the New York Go Center's Iwamoto Memorial Tournament... Directed by Paul Matthews,... Matthews employed the "bonus overtime" system (also known as Fischer overtime), which was new to many participants. Each player began with only ten minutes, but earned twenty seconds for each move, so that players who finish quickly often wind up with twice as much time on their clock as when they began...
- reported by Roy Laird 3k
edgy: The NY Go Center changed the time limit for their tournament this weekend (2007-01-06) to 18 minutes main time and a 15 second increment (it had been 10 minutes/20 seconds). This both allowed a little more time for reflection in the opening and sped up the games somewhat (I think all the games in each round finished in well under 2 hours).
I talked with Roy Laird (NYGC Vice-President) about the timing; he says they've been experimenting with various settings at the Princeton Go Club (if I remember correctly), and that increments under about 15 seconds seem to cause trouble when the players run short of time."