Deckbuilding is a difficult thing. It's usually the most exciting and rewarding part of Magic, but also the most frustrating. Sometimes decks ‘click' and just run well; sometimes an obvious juggernaut on paper ends up being an impotent pile of junk in practice. One of the things to keep in mind when building or tweaking a deck is to identify and strengthen the deck's base.
Bases are an important part of deck building, and one of the key ways to watch how the metagame evolves. Decks don't just fall into place, generally a deck builder starts with a set amount of cards that he feels can be the cornerstone of a deck. While the rest of the deck doesn't have to be directly supporting to your base, it can't interfere with the base working. When two cards in your deck don't synergize, in fact directly counter each other, this counter-synergy is usually solved by removing or replace one of the offending cards.
My Bant deck experienced some counter-synergy. I wanted a big solo attacker, to capitalize on Rafiq of the Many and Exalted bonuses. Elspeth, Knight-Errant was one of those bonuses. I wanted an end-game that could deal with Malakir Bloodwitch and was resistant to removal. Sphinx of the Jwar Isle was one of those end-games. The problem is, Elspeth can't target the Sphinx. Also, with green as the primary color, Elspeth demanded 2 white mana, and the Sphinx demanded 2 blue mana. Two cards that can't work together, and actively push against either other in the mana-base. That's a counter-synergy.
I had to decide what my base was, which cards were critical to my deck. Sphinx was a beater for sure, but so many wins were pulled out by the bonuses granted by Rafiq and Elspeth that they were the base to me, so the Sphinx had to go. In the end, the Sphinx was replaced by Thornling. I decided the 5/5 flier was more replaceable than the white planeswalker.
Think about U/W Control. If someone put a gun to your head and said, you have to remove every copy of Baneslayer Angel or Day of Judgment, what would you do? Luckily, no one is doing that, and those two cards tend to work well together, but if you had to, I imagine most U/W Control players would begrudgingly remove the big Angel over the board clearer. That tells you that Day of Judgment is part of U/W Control's Base. The rest is just supporting cast.
Green/White has had a strong base since the debut of Zendikar, one that is probably more influential on the metagame than anything else. Yeah, Putrid Leech and Sprouting Thrinax probably have more total wins, but neither are them are seen in decks outside of the dominant Jund. However, G/W's base has been the cornerstone of no less than 4 separate lists.
Since the introduction of Zendikar fetchlands, people have quickly discovered the strength of Knight of the Reliquary. Both as a cheap beater in Zoo lists, to a toolbox and protector in Boss Naya / Mythic, KotR has gone from a bargain bin rare to one of the most expensive non-Mythics in Standard. Noble Hierarch has enjoyed the same boost, because Noble Hierarch and Knight of the Reliquary go together like mullets and Dog, The Bounty Hunter.
The original G/W Knightfall was a strong deck utilizing the Hierarch and KotR for both acceleration and fixing, to muscle out big creatures like Baneslayer Angel. The deck has since gone under much iteration, but that base of 4 Hierarchs and 4 KotRs is absolutely rock solid. Splashing blue has brought Rafiq and Rhox War Monk, splashing red has brought Ajani Vengeant and Lightning Bolt, splashing black has brought Maelstrom Pulse. But that base hasn't budged.
Thinking of a deck's base is great for picking up an archetype with the intent of tweaking it. Jund has countless lists out there, tweaking numbers here and there for a variety of guest stars. Playing against Jund as rush or control decks, I felt Putrid Leech and Maelstrom Pulse were the most fearsome cards in the deck. However, as the deck evolved, Jund players targeted Pulse and Leech as some of the more expendable cards, sometimes replacing the Leech with Rampant Growth or Trace of Abundance, and slowly moving to sideboard or even cutting Pulses for new additions like Siege-Gang Commander, Sarkhan the Mad, and Consuming Vapors.
What hasn't changed is Jund's strict loyalty to 4 copies of the Thrinax, Bloodbraid, and Blightning. That's a good mental note as a new player (or a player moving to a new archetype) that if every list you see of a given archetype doesn't budge on a few cards, that tweaking those cards is probably a bad idea. Messing with the base may cause the deck to implode in ways that didn't seem so obvious when you had the deck all laid out.
This is a good practice when making a deck. Lay out all the cards, then force yourself to cut five of the spells. That may not have been too hard. Now cut ten more. Oh yeah, we're going down to around fifteen cards, so now cut five more. What do you see now? You should have 13-16 cards (barring excessive low/high land decks) that still strongly resemble a deck you should be familiar with:
Jund
Mythic
RDW
You couldn't get me to cut anymore cards from those decks. This is a good practice to see which cards are really sacred cows, and which ones are just false idols. I know many RDW players swear by Plated Geopede, but I felt when it came down to the hypothetical gun-to-my-head, my RDW is about hasty dudes and difficult to remove/prevent damage. Jund is about 2-for-1s and efficient removal, which is how you can see some Jund players felt Putrid Leech could be replaced, but Bloodbraid Elf is untouchable.
From the base, you can expand outwards finding cards that support and don't directly conflict with your base. For U/W Control, Day of Judgment was one of the key cards, as was Martial Coup. Everflowing Chalice was a perfect supporting card for that base. It allowed for turn 3 Day of Judgment, as well as earlier Martial Coups. It didn't conflict with anything in the deck, gave it a solid turn 2 play in a deck with no obvious turn 2, and the aftereffect was a card that strongly synergized with the base. Adding in 20 or so supporting cards to your base will always work better than a collection of 35 good but non-synergized cards.
Hopefully you can sit down with that pet deck that just can't seem to make the leap, and analyze what its base is. What cards are supporting that base? Are there better cards to support it, even if on their own they seem like weaker cards? Does you base have an obvious counter that you need to account for or prevent? All of these things are the root of synergy, and the cause of decks going from a pile of Magic cards to revered deck titles. Good luck in your building, perhaps your deck can breakthrough at the next major event!