Generally speaking, the hard cable itself SHOULD be cheaper than the SJTW cord you'd need for a flexible extension. If you're going to go that way, I'd suggest rodent-proofing the run by using armored BX style cable. The size depends on how many amps you want to run through it, I'm no expert on that.
The biggest SJTW cord I've seen readily available in Home Depot, for example, is 10/4. I'm sure bigger stuff can be had, but may be special order, might even have to buy a spool of it.. the 10/4 is pricey as it is, I think it was $5.80 CDN per metre the last time I bought some.
We have a typical transfer switch set-up, one that breaks ALL the connectors going back to the utility, even the common. There's an outside plug-in for the generator, a recessed male plug. It's illegal here to back-feed through a dryer, range, or welder receptacle.
Our transfer switch feeds a generator panel which in turn feeds selected circuits in the house. The switch disconnects the generator panel from the main utility feed before it makes the connection to the generator, so you can't have two supplies actively feeding the house at the same time. A 30 amp connection runs between the main panel and the generator panel to provide power under normal circumstances. I'll take some pics tonight if I remember.
Having the generator feeding the whole house via the regular breaker panel is a problem, because the common wire is often still connected to the utility even when the main breaker is open. As someone mentioned, if you have a problem you can back-feed 220V through the common wire up to the transformer, and then you have serious voltage available to injure or kill someone working on the lines nearby. That's my understanding of it anyway, if I'm wrong someone will point it out.
Sean