The biggest problem is with compatibility. The problem you are going to have most issues with compatibility is the smoke detectors.
Compatibility means "It has been tested and listed to work reliability".
The old panel is a conventional fire alarm panel. Usually, the smoke detectors, heat detectors, and pull stations are also conventional. The heat detectors and pull stations, being just switches, are almost always compatible with any conventional fire alarm system.
Heat detectors though, as they age, might not be as sensitive to heat anymore, so consider replacing the heat detector, it's not expensive.
Pull stations are "exercised" only once a year, so after years, they may be slowly building tarnish on the contacts. When that happens, the pull station starts to be unreliable; the pull station can be pulled and not send in an alarm. Either replace the pull station with a new one, or stand at each one and turn it on and off about 30 times to exercise the contacts (rub the tarnish off the contacts). Make sure it's reliable - replace it if it's not reliable.
The smoke detectors are different. The smoke detectors have electronics inside them so their voltages, currents, and resistances have to match the particular panel that they work with (this is a compatibility issue). If you just replace the old fire alarm panel with a new one, and even if the smoke detectors go into alarm when tested with smoke, the smoke detector / panel combination may not be reliable.
Make sure that any smoke detector you replace is compatible with the new fire alarm panel. It's where you don't replace a smoke detector that you have to do your homework. Get the manufacturers name and model number from each and every smoke detector you are not replacing. Contact the technical support for the make of the new panel being installed, and ask them if the makes and models of the smoke detectors you have are compatible with their fire alarm panel. If you don't do that, you are taking a risk the smoke detectors won't work reliably in case of fire.
While you're at it, get the manufacturer name and model number of the pull stations and heat detectors. When talking to technical support, ask about compatibility, because once in a great while there is some sort of issue there, also.
As far as replacing the panel, there are a number of panels on the market that can be used. EST (formerly Edwards), Silent Knight, Notifier, FCI, and many others are manufacturers that make good conventional fire alarm panels.
Look to make sure that whatever you get has enough input zones, and enough NAC zones (Notification Appliance Circuits or Horn and Strobe Circuits).
Also, make sure the panel you get will be able to send alarms to the monitoring company (Central Station Monitoring or CSM) while at the same time still closing the doors. I don't know how the system is working now with the two alarm signal outputs, so I can't suggest more than "Be Careful and Design This Into the System".