Leona's best defense is also her best offense. I don't think there's any ability in the game that should be leveled first as obviously as her W. In lane, it means that she can be basically untouchable while also dealing very good damage.
Alistar should be used over her if you favor a more defensive lane, because he's still a support character. Leona on the other hand just wrecks offensively with any sort of help. I don't see how her gap closer is worse than Alistars unless Alistar is ganking. A skillshot that passes over minions is a rare boon! All the people who have to hide behind minions when I play Blitz, now they just plain have to keep away from me at all times.
As for runes and items, I go Magic Pen marks, Armor seals, MR Glyphs, and Health quints. Items are standard tanking, Sunfire, Force of Nature, usually don't end up getting more than this per game but the W still brings my defensive stats up to 200 in team fights. I do start with Philo, Hog, Merc Treads. But I get the health regen component first instead of a faerie charm as it is really easy to manage her mana.
As far as the gap closers go, they have similar range (700 for Leona, 650 for Alistar), but Alistar has the advantage of his not being a skillshot at all and thus nearly impossible to screw up(though as an expert at smartcasting Dazzle on minions when I play Taric I guess I can't say that 100%...). I think assuming perfect play for anyone is a bad idea so that's certainly an edge for Alistar, though Leona's range advantage matters sometimes and as far as skillshots go her's is pretty amazing with the minion dodging quality). The main thing that makes it hard for me to imagine many situations where I'd pick Leona over Alistar with both available are the other effects on the abilities, though: Headbutt being able work as a second stun if the opponent is close to a wall in addition to a gap closer, as well as and the incredible utility of knocking opponents into your carry's range/away from their turret/into your turret gives it a pretty big advantage over vs Zenith Blade being simply a gap closer, and Headbutt having the potential to stun multiple targets in one use makes me prefer Alistar version's of those two abilities pretty significantly, both for being a bully in lane and for teamfighting(particularly for initiation). Alistar can kind of imitate the way Leona does things with Headbutt->Pulverize, but Leona lacks a lot of what he can do with the impact on multiple targets and the knockbacks. Some of Alistar's flash combos are kind of a noteworthy separator too, since he gains a lot of effective range and initiation ability.
Alistar's E giving his laning perhaps the last strong sustain in the game is a pretty big kicker comparing the two as well(and it's a cheap Trample activation all game), giving him the flexibility of being able to play more passively in lane for a while if things take a bad turn, which is something Leona has no answer to. She instead has her W which makes her more reliably tanky than the ult-reliant Alistar and eventually lets her pass him in damage, since while Alistar's base damages are higher Eclipse gains more per level than Pulverize. From an damage perspective I still like Alistar better, since Leona doesn't start pulling away until the damage either of them do is starting to get bad regardless in the mid-game. Alistar Headbutt+Pulverizing people the first 3 or 4 levels is an awful lot of damage with the added benefit of them locked in place the entire time to increase the time on target of Alistar and his carry, and with the physical damage Reds Alistar can afford to use to boost his early game helping out he can pressure a squishy awfully hard on his own(since the AP scaling nerfs and the relatively low base damages on his abilities have made mpen kind of pointless on Alistar now, and as you suggested Mpen is more necessary on Leona preventing her from keeping pace there). I like Alistar's early game damage better even once Eclipse gets a few levels to bridge the gap just because Alistar is so much better at locking a target in place and preventing incoming damage to his carry or himself with the potential double stun, but it's noteworthy that Leona is better at shrugging of damage if you don't have a wall to Headbutt people into and that she provides more damage herself once she hits level 5 and jumps ahead again at 6 with her Ult being more offensive and adding more control.
Leona is obviously more reliably tanky as the game wears on than Alistar, but assuming your team is still running the usual strategy bottom where it is your lane partner who needs all the farm to avoid playing the game as two half characters instead of one good one, it's tough for either Leona or Alistar to end up getting anywhere near unkillable(though both can mostly do it temporarily with Eclipse and Unbreakable Will, and Eclipse has the advantage of always been up when you need it in exchange for a shorter duration), which mitigates some of the late game advantage Leona would otherwise have over Alistar, though I haven't gotten there as Leona myself enough to compare accurately. It's kind of surprising how similar they are as far as abilities fulfilling roles(Zenith Blade vs Headbutt, Shield of Daybreak vs Trample, Eclipse vs Unbreakable Will, hell, even Sunlight vs. Trample), but without farm to break Leona away late game I think Alistar's CC and lane sustain makes him a better pick in bottom all game if you aren't going to get a significant amount of farm(and I'm somewhat skeptical of team comps where you are). I haven't mentioned Leona's ult enough to this point in the post, but it is obviously noteworthy as the game wears on as well, since the one ability that isn't similar between the two of them becomes a big win for Leona as Triumphant Roar becomes pretty weak late in the game and Leona's ult provides some supplemental damage and CC.
I don't mean this suddenly kinda long post as a rip on Leona at all, because with as good as Alistar is right now being nearly as good as he is still easily puts Leona as one of the best fifth wheel options, I think -- she's probably better than Taric at his job, selecting Leona over Janna and Sona would depend more on your team needs than their relative power, and Soraka requires some kind of bizarre laning combinations to be worth it herself as a support atm(I want to play around with AP carry+Support Soraka bot but haven't had the chance to work the team comp yet), even if I'm still a stubborn Alistar main comparing the two of them, I guess. Leona's not a true support the way people are seeing them right now, since when they see support they think "sustain," but with Riot trying to stomp that out bottom lane will probably shift more toward champs than can still be productive with limited farm, since like Kinneas posted a few posts ago, there's still five heroes for four effective lanes and getting two half heroes out of bot is almost never a good idea. I think that's what Riot wants anyway, since playing like Alistar and Leona do makes support more "interactive" or whatever, and if things shift that way Leona is due for some more popularity imo.
As far as the advice, I'll definitely start with Regrowth Pendant + Pot next time I play with her. I hate the flexibility you lose starting with no wards bottom, but I don't think there's really a viable alternative with Leona since Faerie Charm does nothing but make a down payment on Philos and the crystal for HOG is too expensive. I'm a whore for Avarice quints and will probably keep trying to sneak at least a couple of those over the health quints, though... I just have a hard time saying no to them on characters where I want/need to be doing a lot of warding or picking up Oracles or whatever and know I won't be seeing a lot of farm, since it leaves me that extra gold to buy an item later in the game that will help my tankiness a lot more than the health quints would past the first few levels of the game where they really shine.
