Rune Factory Frontier is the sequel to the first Rune Factory. Different stories, towns, villagers, et cetera, and they are both rather awesome.
As for not playing the game before in the series such as Island of Happiness and Tree of Tranquility, I must say that you probably wouldn't miss a whole lot, but you would still miss a bit. I do admit both SI and AP look spectacular and definitely do topple their predecessors. I would feel zero guilt suggesting you to play Sunshine Islands and to skip Island of Happiness since it really does lighten up on the difficulty Island of Happiness gives you in the very beginning.
As for skipping Tree of Tranquility... I think it just has a separate little charm from Animal Parade. The different towns/areas and random/heart events that occur always have me buying each Harvest Moon, but even I am starting to come around that nothing is as spectacular in ToT while comparing it to AP. While no Witch is in Tree of Tranquility I will tell you what it does have: Short Luna. Luna is much taller in Animal Parade. Also your child will look more like you in Tree of Tranquility while the children in Animal Parade will always take after your wife's hair and eye color. Yup, you can have pink haired boys even in AP. And as said earlier too like all other Harvest Moon games that share a cast the heart events will differ along with the dialogue as you raise the characters affection. Ah, and you can have five pets in ToT rather than AP's four pet limit; It is something that I myself found to be rather nice.
You could skip A Wonderful Life, but I thought you would like to know it is rather fast paced so it wouldn't take too incredibly long to complete. Ten day seasons which is forty days a year over the course of six years that have a slight story to them. No festivals take place which is a bit of a bummer, it is mainly about growing old with the villagers around you and raising your kid as
he grows. Or
she If you buy AWL: Special Edition
(which is laggy in comparison) or Another Wonderful Life which allow you to have a female daughter. Also time moves in doors and the farming isn't anything too special. I actually found it a touch annoying since the water dries away some days and you must water again. No tool upgrades either.
Also SI, IoH, and the Rune Factories are all 3D on the DS. The Rune Factory titles have mainly 2D worlds though. And Harvest Moon 64 is entirely 3D in it's 64 bit glory.
If there is a game I can warn you of on your list though it would be Harvest Moon DS. Gathering sixty sprites takes some extreme work, ranging from one year to two years in game depending on how tough you work. I have heard a few people who it took three years for as well. I encourage you to take a skim over the sprite page and see if how you get them doesn't sound too incredibly tedious for you. Just click the link that says 101 Sprites:
http://www.fogu.com/hm6/ I like my Harvest Moon games to relax me so I didn't purchase this one. And as you may hear around here, it is the glitchiest Harvest Moon Natsume has ever localized. Game-breaking things are present and accounted for.
As for why it only has individual boards for hand held games it is because that is what the forum was primarily created for as Nina said. The hand held games of Harvest Moon. River King as well back when it was popular, but that seems to have faded with time.