Wouldn't you rather pay $50 – $100 to file your taxes with softwarethan face the long arm of Uncle Sam's fee schedule? Or, even better, file easier returns for free with the IRS Free File Alliance if you earn below certain annual thresholds.
Penalties are the worst. They're not any better coming from the federal government. For failing to file a return when you are technically required to do so, they slap you with a late-filing penalty worth 5% of the tax owed per month in most circumstances.
A substitute return won't include all the details you'd like shown about your tax picture, costing you money for not claiming applicable deductions, credits, or other tax items which benefit your bottom line.