if they can't find one with what you want, tell them to order it for you or you will buy elsewhere. they just want to unload their inventory on you. you can go to nissanusa.com, and build your own frontier, with any options you want. i don't know if it applies to the frontier, but sunroofs usually eliminate the overhead console. the microfiber would probably be easier to clean, but unless you plan to get inside while filthy, you probably won't need it. if you need a roof rack, im sure you can buy an aftermarket one for less than the factory option. tow packages usually consist of an auxillary oil/transmission cooler, sometimes they come with lower gears, and upgraded suspensions. if you don't plan to tow all the time, just get a hitch installed at a local hitch shop, but if you are going to be towing, get the factory one. i don't know for sure about the frontier, just usually that package comes with the coolers. i'd say to ask the dealer, but they usually don't know shit. leather is standard on the Titan LE, and they were trying to say it was extra cost.
www.nissanusa.com is your friend. research the truck before you buy. go armed with the MSRP.
www.edmunds.com and see what the true market value is. get quotes from multiple dealers. do your homework, and get a good deal on the truck YOU want, not what the dealer wants you to buy.