I would check first why the A/C is on the roof - required in your area by code or subdivision covenant for appearance and noise control, maybe. That would certainly impact your decision.
Assuming you have forced air furnace like most houses in SoCal, then moving the units without reason serves little purpose. Your rooftop unit is possibly less efficient than a ground-mounted unit in your area since the ambient temperature on the roof is much higher and you are not in an area with significant prevailing winds (unless up in the hillside/Sierra Madres area) except for the hot Santa Anas (which provide no cooling), but if there is a lot of cost in ducting changes to swap to a ground-mounted unit it might not pay off.
Certainly, in your environment you are looking at a small furnace which is not used too much (although reaching heating temperature outside almost 12 months a year), so spending a lot of money on efficiency would not save you much there, especially if natural gas fired as I assume - so I would just go with a good brandname 80% efficiency unit for that. The A/C is where you should be concentrating your research regarding the cost-benefits of higher efficiency units, because you have about 8 A/C months a year, and three well into the 90's for average daytime high - not to mention the smog which makes people keep their windows closed a lot of the time, hence more air conditioning demand.
SCE, TheGasCompany, and the US Dept of Energy EnergyStar program all have good website info on typical cost-benefits of more efficient units, and the utilities have info on the cost of your power and gas on your bill so you can use actual energy costs in figuring your expected cost. Bear in mind to use only the energy charge parts, not including the fixed flat monthly service rate or fixed government charges which does not change with usage. May be several types of charges based on energy usage, and some government fees or taxes related to that too - if you can not figure out which to use, call the energy conservation office or billings office at your utility and they should be able to explain it to you - as can the webpages explaining your bill (also sometimes on the back). Haven't used those utilties for quite awhile so don't know what they have on their bills now.
Like prior comment said, contact several HVAC contractors with good reviews and ratings, then talk to them about brand and configuration possibilities and have them take measurements and do the required Manual calculations to size your system but tellthem NOT to prepare a bid right off, then after talking to about 3 decide what efficiency and type of unit you want and brands you will accept, THEN call all back and have them all bid on the same general system requirements (furnace Btu and A/C tons and SEER rating, etc) (though they will likely bid different brands).
IF you are planning on staying in this house for a long time or see little chance of a move in the future so this replacement is a long-term investment for you, I would consider a higher efficiency unit like SEER 16-18 range for your area. You are in a serious A/C environment much of the year and SoCalEdison rates certainly are not going to be going down, and with San Onofre being abandoned and Diablo Canyon cutting back power, Hoover and Glen Canyon Dams producing less power due to the water shortages, and the Four Corners area coal plants being pinched by the new coal air pollution regulations, your rates will be increasing even more - quite likely dramatically in the next few years. I know in our area we have had 40% electricity and 48% gas consumption rate increases this year already and over 100% total increase in the past 3 years or so, and more coming.