First off, it's not a 6k price difference. You have to compare apples to apples with options on the car. The SE-R shipped with every available option except the NAVI package which wasn't possible due to the guage pod for the SE-R, and the Satellite Radio option. So, let's compare apples to apples based on pricing from nissannews.com:
2005 Altima SE-R MSRP: 29,350
2005 Altima SE MSRP: 23,300
Now, let's add the options to the SE to compare apples to apples:
Leather Sport Package: 3,900
EC Mirror w/Compass: 220
So, we'll now add 4,120 to the base price of the SE which brings us to 27,420 with the same options. Price difference is now 29,350 minus 27,420 which equals 1930 dollars difference.
Please note I've not added in any options that both cars offer, such as TCS/side airbags, satellite radio, etc. as the options prices are the same for each car so there's no point in doing so.
So, for that 1930 dollars difference in MSRP, we received:
18" forged alloy lightweight wheels w/225/40ZR18 S03 tires
Sport suspension package including performance-tuned suspension with recalibrated front struts and rear shocks, stiffer front and rear springs and thicker front and rear stabilizer bars
Sport braking package including larger 12.6x1.1-inch front brakes with silver painted front and rear calipers, SE-R logo on front calipers
Interior package including custom sport leather interior w/dark chrome trim, heated front seats, aluminum pedals including dead pedal, three guage instrument cluster
Appearance package including front fascia, rear spoiler/bumper, and side sills, headlight/taillight unique color treatment, unique fog lights
Perfromance package including high flow exhaust w/larger diameter chrome tipped dual exhaust, tuned ECU, available 6-speed transmission or performance tuned 5-speed automatic (both with better performance gearing over the standard Altima models)
Now, for an extra 1930 dollars, that seemed like a pretty good deal to me. This is the analysis I did when I looked at both the SE and the SE-R for myself. Now, please understand that if you don't care about the options and have no issues rolling around in a stripped down SE, then the 6k price difference is valid, but in my view, you can't make that comparison without pointing out the underlying assumptions in making such a comparison as I've done here.
Heck, the OEM 18" forged wheels, even through a discount parts shop, run 500 a pop (normally 650 thru Nissan), so that's 2k in cost alone as compared to the 1930 dollar MSRP price difference.
It's also worth noting the the 5-speed performance tranny option for the SE-R is a free upgrade, it costs an extra 650 dollars on the SE models, further narrowing the price comparison for for auto-trannied cars.
Now, I'm not arguing either car is inherently better or worse in any way, just pointing out how I did my own comparison when I shopped for the car I currently have. To each his own I always say, if you are happy with your current ride, that's all that matters. That said, for a price difference of only 1930 dollars MSRP, it seemed to me at least, that you actually get some decent upgrades for under 2k price difference. If you were to attempt to buy these same options aftermarket, they would cost you considerably more than 2k, probably closer to the 6k price difference in reality when taking into account the appearance, performance, interior, suspension, and braking modifications.