All Oil, Gas and Mineral Leases are bi-latteral agreements and can be amended, added to and deleted from in any number of ways. I know - I've negotiated them for over 30 years on behalf of oil and gas companies.
Bonus consideration paid for leases in the Niobrara play will continue to climb over the next few years. A little patience on your part may result in a much greater amount of Bonus monies being offered in the coming months.
Do an online search of the recent State and Federal Lease Sales in your area - you may be pleasantly surprised at the amounts being paid to the State and the Federal Government for leases on land just like yours.
Never give anybody a two year option to extend for no additional Bonus payment. I've never even heard of such a thing - the Landman should be ashamed of himself. An extension of a primary term without adequate consideration offered and accepted might not even be legally binding.
I would suggest a substantially higher amount of additional bonus for any additional years - perhaps 3 times what they neogtiate for the first 3 years. That is, if you allow them any option to extend at all (I would not).
It's your land and your minerals and you need to have all of your rights completely protected at the point of signing, because once you've committed the company is highly unlikely to agree to any further amendment(s) your lease.
What do you do with the land? There are environmental indemnity issues, damage and loss of use issues, drainage concerns, roadway and padsite construction and placement issues, fencing, gates, cattle guards, water wells - all sorts of issues you should address before signing anything.
Royalty to be retained, Pugh Clause, Depth Severance Clause, Free Royalty Clause - these and other issues should also be considered before signing. And, yes, Warranty Clauses can be amended or even completely stricken from the lease - it's done all the time.
If you have not already done so, I strongly advise you to consult an Oil & Gas Attorney before continuing any further negotiations. Even if you have to travel a bit and his or her services cost more than you expect, it will be worth it for your peace of mind.
Hope this helps -
Charles Emery Tooke III
Certified Professional Landman
Fort Worth, Texas