It's my contention that upgraded peripheral-tangibles, those environmental features like upholstery, trim, and even styling, are NOT a viable solution for long term brand identity. Although I'm not a nuts & bolts person, it seems obvious to me that mechanical differentiation is needed.

1. suspensions
This could be the most important variable. Properly designed these could be bolt-on components, important brand identity features, that would not impact the cost of the platform itself. Lincoln's would be an automatically adaptive, intelligent, active suspension. Mercury would have manually adjustable settings (standard), giving a ride that could range from cushy boulevard cruising to a rigid sport setting that could handle the 'twisties' as well as most sport-sedan icons. Ford would continue to use static tuned suspension parts geared toward the specific role of each model.

In addition, an adjustable ride height system could be offered on awd suv/crossovers, then spread to top-of-the-line passenger cars, and possibly/eventually to all models. Our cities' deteriorating infrastructure is converting our roads to off-roads. And even a low slung sports model can use some added height when stuck in heavy traffic. This capacity is currently offered on Audi Allroads and top LandRovers. Can FML build on the LR system? It would probably necessitate a stability control system and require a speed-sensitive mode (as well as several driver-selected settings) which would also return the vehicle to defaults when the situation becomes unsafe.

update:
If a new Rwd architecture is being developed for Lincoln and FordAu-FordNA, in order to sufficiently different the platform(s), three suspension versions may be the way.
Lincoln: super sophisticated active electronic damper control that automatically provides the smoothest (not the same as softest) ride possible.
FordAu's heavy-duty modules could also be used for law enforcement or livery in NA while
FordNA's specialty models (Mustang-Falcon-Thunderbird) benefit from a strong but lighter version.

2. engines
This is where Ford comes first. They get everything. Econo, 'good' power, hP with a capital P, and "OMG can this thing move!"
Mercury generally goes with the middle 2 and Lincoln really only needs the 'hP' so it never has to really think about it.
Brand Versions - A middle-sized 5.0 version of the 4.6/5.4 v8, just for Mercury. Forced induction option for most engines/models (SVT & Mercuryspeed?). The 3.8L 280-300hp v6 instead of the 3.5 for Lincoln (also SVT500 and Thunderbird). The Yamaha 4.4 v8 for Lincoln - every Lincoln should have a v8 available! Possibly a 7.0 liter v12 (double 3.5 v6) to replace the v10.
(yeah, this was written pre-Katrina)
Diesels - If the US follows the european market, diesels will soon be a large % of total sales.
I hope FML is hard at work on the diesels so they're READY for 2007 & beyond...